library(multiMiR)
## Welcome to multiMiR.
## 
## multiMiR database URL has been set to the 
## default value: http://multimir.org/
## 
## Database Version: 2.3.0  Updated: 2020-04-15
library(clusterProfiler)
## 
## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
## 
## Please cite:
## 
## Guangchuang Yu, Li-Gen Wang, Yanyan Han and Qing-Yu He.
## clusterProfiler: an R package for comparing biological themes among
## gene clusters. OMICS: A Journal of Integrative Biology 2012,
## 16(5):284-287
## 
## Attaching package: 'clusterProfiler'
## The following object is masked from 'package:multiMiR':
## 
##     select
## The following object is masked from 'package:stats':
## 
##     filter
library(org.Hs.eg.db)
## Loading required package: AnnotationDbi
## Loading required package: stats4
## Loading required package: BiocGenerics
## 
## Attaching package: 'BiocGenerics'
## The following objects are masked from 'package:stats':
## 
##     IQR, mad, sd, var, xtabs
## The following objects are masked from 'package:base':
## 
##     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
##     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
##     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
##     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
##     Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
##     tapply, union, unique, unsplit, which.max, which.min
## Loading required package: Biobase
## Welcome to Bioconductor
## 
##     Vignettes contain introductory material; view with
##     'browseVignettes()'. To cite Bioconductor, see
##     'citation("Biobase")', and for packages 'citation("pkgname")'.
## Loading required package: IRanges
## Loading required package: S4Vectors
## 
## Attaching package: 'S4Vectors'
## The following object is masked from 'package:clusterProfiler':
## 
##     rename
## The following object is masked from 'package:utils':
## 
##     findMatches
## The following objects are masked from 'package:base':
## 
##     expand.grid, I, unname
## 
## Attaching package: 'IRanges'
## The following object is masked from 'package:clusterProfiler':
## 
##     slice
## The following object is masked from 'package:grDevices':
## 
##     windows
## 
## Attaching package: 'AnnotationDbi'
## The following object is masked from 'package:clusterProfiler':
## 
##     select
## 
library(stringr)
library(ggplot2)

0. Loading of Results

A. List of all Gene names in the dataset

gene.names = readRDS("data/derived/unique_gene_names.rds")

B. Selected Features

results.mofa = readRDS("data/sel_features/results_mofa_extracted_by_bic.rds")
sel.features = results.mofa
sel.features
## $`1f`
## $`1f`$Factor1
## hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1193   hsa-mir-1197    hsa-mir-127 
##     -0.7629508     -0.7462546     -0.6264293     -0.8177493     -0.6107271 
##    hsa-mir-134    hsa-mir-136    hsa-mir-137    hsa-mir-154    hsa-mir-299 
##     -0.5900502     -0.6225595      0.3615164     -0.6243017     -0.6020226 
##    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2    hsa-mir-337 
##     -0.7085735     -0.7171871     -0.9023781     -0.6506600     -0.4522194 
##    hsa-mir-369    hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2   hsa-mir-376b 
##     -0.5855907     -0.6299468     -0.6462057     -0.7213440     -0.6056218 
##   hsa-mir-376c    hsa-mir-377    hsa-mir-379    hsa-mir-380    hsa-mir-381 
##     -0.5984895     -0.6137607     -0.5998633     -0.7333177     -0.5946947 
##    hsa-mir-382    hsa-mir-409    hsa-mir-410    hsa-mir-411    hsa-mir-412 
##     -0.6338445     -0.6219059     -0.6434716     -0.6958073     -0.5501088 
##    hsa-mir-431    hsa-mir-432    hsa-mir-433    hsa-mir-466    hsa-mir-485 
##     -0.6248299     -0.6426433     -0.6436876      0.4015545     -0.6906152 
##   hsa-mir-487a   hsa-mir-487b    hsa-mir-493    hsa-mir-494    hsa-mir-495 
##     -0.7452065     -0.6615326     -0.5307040     -0.6393844     -0.5588490 
##    hsa-mir-496    hsa-mir-539    hsa-mir-541    hsa-mir-543    hsa-mir-544 
##     -0.6347435     -0.6248115     -0.6876863     -0.6419155     -0.4143495 
##    hsa-mir-654    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668 
##     -0.5842991     -0.7051487     -0.7722097     -0.6770739     -0.8606763 
##    hsa-mir-758    hsa-mir-770    hsa-mir-889 
##     -0.5809780     -0.7888620     -0.6473752 
## 
## 
## $`2f`
## $`2f`$Factor1
##   hsa-mir-1258   hsa-mir-135b    hsa-mir-506    hsa-mir-508  hsa-mir-509-3 
##     -0.2733195      0.2678525     -0.3185482     -0.2774065     -0.2687342 
##    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2   hsa-mir-513b   hsa-mir-513c 
##     -0.3650144     -0.3297462     -0.3227300     -0.3234853     -0.2877525 
##  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3    CTNNA1.R2Gn      G6PD.RPPA 
##     -0.3280582     -0.3258505     -0.3244563     -0.2694667     -0.4501249 
##    IGFBP2.RPPA     RBM15.RPPA       ATM.RPPA      FASN.RPPA    INPP4B.RPPA 
##      0.3018783      0.7999696      0.3250985      1.0536463     -0.4189671 
##      TSC1.RPPA      TTF1.RPPA       VHL.RPPA     PRDX1.RPPA      XBP1.RPPA 
##      0.4269544     -0.3765308     -0.5905985     -0.5384414     -0.3626753 
##      MSH6.RPPA      TFRC.RPPA      MSH2.RPPA     PREX1.RPPA 
##      0.7180545      0.4532162      0.2702868     -0.4629907 
## 
## $`2f`$Factor2
## hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1193   hsa-mir-1197    hsa-mir-127 
##     -0.8148004     -0.7998948     -0.6412522     -0.8151468     -0.6292322 
##    hsa-mir-134    hsa-mir-136    hsa-mir-137  hsa-mir-138-1    hsa-mir-154 
##     -0.5866563     -0.6456195      0.3196321      0.2904333     -0.6491630 
##    hsa-mir-299    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2 
##     -0.6144646     -0.7357216     -0.7650560     -0.9230492     -0.6390089 
##    hsa-mir-337    hsa-mir-369    hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2 
##     -0.4441141     -0.5933784     -0.6397646     -0.6545057     -0.7125216 
##   hsa-mir-376b   hsa-mir-376c    hsa-mir-377    hsa-mir-379    hsa-mir-380 
##     -0.6112866     -0.6071882     -0.6177324     -0.6089270     -0.7394387 
##    hsa-mir-381    hsa-mir-382    hsa-mir-409    hsa-mir-410    hsa-mir-411 
##     -0.6096473     -0.6500180     -0.6377656     -0.6699741     -0.7572727 
##    hsa-mir-412    hsa-mir-431    hsa-mir-432    hsa-mir-433    hsa-mir-466 
##     -0.5592501     -0.6241728     -0.6549299     -0.6954934      0.3784283 
##    hsa-mir-485   hsa-mir-487a   hsa-mir-487b    hsa-mir-493    hsa-mir-494 
##     -0.7505666     -0.7678460     -0.6853095     -0.5395591     -0.6570549 
##    hsa-mir-495    hsa-mir-496    hsa-mir-539    hsa-mir-541    hsa-mir-543 
##     -0.5905014     -0.6631960     -0.6498181     -0.6976724     -0.7016385 
##    hsa-mir-544    hsa-mir-577    hsa-mir-585    hsa-mir-654    hsa-mir-655 
##     -0.4388437      0.2662390      0.2703556     -0.5988272     -0.7417666 
##    hsa-mir-656    hsa-mir-665    hsa-mir-668    hsa-mir-758    hsa-mir-770 
##     -0.7694766     -0.6560661     -0.9011633     -0.5863475     -0.7715128 
##    hsa-mir-889 
##     -0.6736458 
## 
## 
## $`3f`
## $`3f`$Factor1
## hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1193   hsa-mir-1197   hsa-mir-1258 
##     -0.7649038     -0.7472290     -0.6257883     -0.8151400      0.3117462 
##    hsa-mir-127    hsa-mir-134    hsa-mir-136    hsa-mir-137  hsa-mir-138-1 
##     -0.6123154     -0.5905554     -0.6246587      0.3602757      0.2837456 
##    hsa-mir-154    hsa-mir-299    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1 
##     -0.6272125     -0.6030781     -0.7104303     -0.7207944     -0.9035395 
##  hsa-mir-329-2    hsa-mir-337    hsa-mir-369    hsa-mir-370 hsa-mir-376a-1 
##     -0.6551830     -0.4531594     -0.5869315     -0.6311082     -0.6467226 
## hsa-mir-376a-2   hsa-mir-376b   hsa-mir-376c    hsa-mir-377    hsa-mir-379 
##     -0.7206759     -0.6064602     -0.5995535     -0.6144270     -0.6010460 
##    hsa-mir-380    hsa-mir-381    hsa-mir-382    hsa-mir-409    hsa-mir-410 
##     -0.7321005     -0.5965367     -0.6356706     -0.6233494     -0.6455569 
##    hsa-mir-411    hsa-mir-412    hsa-mir-431    hsa-mir-432    hsa-mir-433 
##     -0.7016670     -0.5505418     -0.6259743     -0.6441280     -0.6460453 
##    hsa-mir-466    hsa-mir-485   hsa-mir-487a   hsa-mir-487b    hsa-mir-489 
##      0.4156560     -0.6992923     -0.7463014     -0.6639803      0.2486635 
##    hsa-mir-490    hsa-mir-493    hsa-mir-494    hsa-mir-495    hsa-mir-496 
##      0.2658478     -0.5316300     -0.6413019     -0.5615859     -0.6368647 
##    hsa-mir-506    hsa-mir-507    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 
##      0.2518729      0.2209553      0.3320070      0.2278679      0.2806987 
##   hsa-mir-513b   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3 
##      0.2429859      0.2522876      0.2285119      0.2285385      0.2270829 
##   hsa-mir-517a    hsa-mir-539    hsa-mir-541    hsa-mir-543    hsa-mir-544 
##      0.2227962     -0.6271768     -0.6866341     -0.6493149     -0.4138828 
##    hsa-mir-577    hsa-mir-585    hsa-mir-605    hsa-mir-653    hsa-mir-654 
##      0.2761759      0.2673895      0.2718495      0.2246087     -0.5858963 
##    hsa-mir-655    hsa-mir-656    hsa-mir-665    hsa-mir-668    hsa-mir-758 
##     -0.7073773     -0.7716958     -0.6887911     -0.8602373     -0.5819465 
##    hsa-mir-770    hsa-mir-889      G6PD.RPPA      FASN.RPPA    INPP4B.RPPA 
##     -0.7952202     -0.6500319      0.2404191     -0.2885815      0.2408990 
##     PRDX1.RPPA 
##      0.2636502 
## 
## $`3f`$Factor2
##   hsa-mir-1226   hsa-mir-1258   hsa-mir-135b    hsa-mir-139    hsa-mir-182 
##      0.2233851     -0.4302970      0.2926786      0.3497486      0.2766422 
##    hsa-mir-183    hsa-mir-184    hsa-mir-187 hsa-mir-196a-1 hsa-mir-196a-2 
##      0.2841530     -0.2375634      0.2371328      0.2896094      0.2599002 
##   hsa-mir-196b   hsa-mir-2114  hsa-mir-218-1  hsa-mir-218-2   hsa-mir-3166 
##      0.2862292     -0.3140284      0.2630450      0.3165759      0.3280705 
##   hsa-mir-3170   hsa-mir-3655    hsa-mir-383   hsa-mir-3917   hsa-mir-3923 
##      0.2912757     -0.3138855      0.2283583      0.2294467      0.2732425 
##    hsa-mir-411    hsa-mir-485    hsa-mir-506    hsa-mir-507    hsa-mir-508 
##     -0.2500918     -0.2914957     -0.8235410     -0.8798237     -0.7841521 
##  hsa-mir-509-1  hsa-mir-509-2  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 
##     -0.7517999     -0.7475504     -0.7555578     -0.9424875     -0.8275008 
## hsa-mir-513a-2   hsa-mir-513b   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2 
##     -0.9246400     -0.7336730     -0.7541221     -0.8465889     -0.8511083 
##  hsa-mir-514-3   hsa-mir-514b    hsa-mir-543    hsa-mir-615    hsa-mir-887 
##     -0.8518621     -0.7302340     -0.2690902      0.2833678      0.2814917 
##    hsa-mir-92b     hsa-mir-96     RBM15.RPPA      PTEN.RPPA      TSC1.RPPA 
##      0.2259010      0.2418153      0.3592209      0.2233962      0.3981680 
##      TTF1.RPPA       VHL.RPPA     PREX1.RPPA 
##     -0.2463980     -0.4164379     -0.2251980 
## 
## $`3f`$Factor3
## named numeric(0)
## 
## 
## $`5f`
## $`5f`$Factor1
##  STMN1.R2Gn   CDK1.R2Gn  CCNB1.R2Gn   G6PD.RPPA IGFBP2.RPPA  RBM15.RPPA 
##   0.1986635   0.2107954   0.1914999  -0.2784869   0.2231534   0.5884744 
##  GATA3.RPPA    ATM.RPPA  BRCA2.RPPA   FASN.RPPA INPP4B.RPPA   TSC1.RPPA 
##  -0.3249034   0.2610943  -0.2230770   0.9309107  -0.3657546   0.2800193 
##   TTF1.RPPA   CDK1.RPPA    VHL.RPPA  PRDX1.RPPA   XBP1.RPPA  GAPDH.RPPA 
##  -0.2885557  -0.2259187  -0.4192049  -0.4660874  -0.3349707   0.3190805 
##   MSH6.RPPA  MYH11.RPPA   TFRC.RPPA   MSH2.RPPA  PREX1.RPPA 
##   0.6825490  -0.2656290   0.4747938   0.2681282  -0.3944828 
## 
## $`5f`$Factor2
## hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1193   hsa-mir-1197   hsa-mir-1258 
##     -0.7585875     -0.7579153     -0.6106161     -0.8063115      0.3553090 
##    hsa-mir-127  hsa-mir-129-2   hsa-mir-1291    hsa-mir-134 hsa-mir-135a-1 
##     -0.6067963      0.1967504      0.1958421     -0.5614834      0.2031226 
##    hsa-mir-136    hsa-mir-137  hsa-mir-138-1    hsa-mir-154    hsa-mir-205 
##     -0.6274709      0.3337672      0.2560318     -0.6174549      0.2176485 
##    hsa-mir-299    hsa-mir-323   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2 
##     -0.5925601     -0.7101262     -0.7288977     -0.9205374     -0.6773367 
##    hsa-mir-337    hsa-mir-33b    hsa-mir-369    hsa-mir-370 hsa-mir-376a-1 
##     -0.4617565      0.1884892     -0.5758965     -0.6270633     -0.6579611 
## hsa-mir-376a-2   hsa-mir-376b   hsa-mir-376c    hsa-mir-377    hsa-mir-379 
##     -0.6664014     -0.5960246     -0.5905546     -0.6045995     -0.5757390 
##    hsa-mir-380    hsa-mir-381    hsa-mir-382    hsa-mir-383   hsa-mir-3909 
##     -0.7120968     -0.5708246     -0.6251879     -0.1941954      0.1866493 
##   hsa-mir-3922    hsa-mir-409    hsa-mir-410    hsa-mir-411    hsa-mir-412 
##      0.1996993     -0.6185533     -0.6469681     -0.6913067     -0.5558614 
##    hsa-mir-431    hsa-mir-432    hsa-mir-433    hsa-mir-466    hsa-mir-485 
##     -0.6398707     -0.6475080     -0.6672985      0.4424094     -0.6710682 
##   hsa-mir-487a   hsa-mir-487b    hsa-mir-488    hsa-mir-489    hsa-mir-490 
##     -0.7257411     -0.6719176      0.1999765      0.2445012      0.2758687 
##    hsa-mir-493    hsa-mir-494    hsa-mir-495    hsa-mir-496    hsa-mir-499 
##     -0.5388712     -0.6089900     -0.5462614     -0.6448792      0.2226947 
##    hsa-mir-506    hsa-mir-507    hsa-mir-508  hsa-mir-509-1  hsa-mir-509-2 
##      0.3840058      0.3750684      0.3639676      0.3490401      0.3463436 
##  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2   hsa-mir-513b 
##      0.3466478      0.4551782      0.3447721      0.4144709      0.3474466 
##   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3   hsa-mir-514b 
##      0.3822525      0.3548202      0.3572057      0.3565667      0.3278773 
##   hsa-mir-517a   hsa-mir-518f   hsa-mir-520a   hsa-mir-526b    hsa-mir-539 
##      0.2582380      0.1856824      0.2191678      0.1998557     -0.6358414 
##    hsa-mir-541    hsa-mir-543    hsa-mir-544    hsa-mir-577    hsa-mir-585 
##     -0.6879424     -0.6286093     -0.3783225      0.2676026      0.2643647 
##    hsa-mir-605    hsa-mir-654    hsa-mir-655    hsa-mir-656    hsa-mir-665 
##      0.2569081     -0.5912489     -0.6985868     -0.7680615     -0.7129604 
##    hsa-mir-668    hsa-mir-758    hsa-mir-770    hsa-mir-889   hsa-mir-891a 
##     -0.8759764     -0.5601472     -0.8024955     -0.6434183      0.1956581 
## 
## $`5f`$Factor3
## hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1197   hsa-mir-1226  hsa-mir-124-3 
##     -0.2693898     -0.2153963     -0.1982752      0.2103746      0.2058201 
##   hsa-mir-1249  hsa-mir-1255a   hsa-mir-1258   hsa-mir-135b    hsa-mir-139 
##      0.2124197      0.1936285     -0.3686553      0.2490502      0.3217925 
##    hsa-mir-182    hsa-mir-183    hsa-mir-184    hsa-mir-187 hsa-mir-196a-1 
##      0.2398068      0.2430847     -0.2246937      0.2105549      0.2294495 
## hsa-mir-196a-2   hsa-mir-196b    hsa-mir-206   hsa-mir-2114  hsa-mir-218-1 
##      0.2111500      0.2401641      0.1875115     -0.2789480      0.2197055 
##  hsa-mir-218-2   hsa-mir-3166   hsa-mir-3170    hsa-mir-323   hsa-mir-323b 
##      0.2598653      0.2902097      0.2486504     -0.1916817     -0.2305173 
##    hsa-mir-338   hsa-mir-3655 hsa-mir-376a-2    hsa-mir-379    hsa-mir-380 
##      0.1898335     -0.2836783     -0.2643668     -0.1870428     -0.1919658 
##    hsa-mir-381    hsa-mir-383   hsa-mir-3917   hsa-mir-3923    hsa-mir-410 
##     -0.1987551      0.1977353      0.2001151      0.2339307     -0.1858580 
##    hsa-mir-411    hsa-mir-433    hsa-mir-485   hsa-mir-487a    hsa-mir-494 
##     -0.2921805     -0.2019031     -0.3417393     -0.2342592     -0.2366182 
##    hsa-mir-495    hsa-mir-506    hsa-mir-507    hsa-mir-508  hsa-mir-509-1 
##     -0.1956948     -0.7359853     -0.8076562     -0.7308223     -0.7148668 
##  hsa-mir-509-2  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 
##     -0.7105480     -0.7097014     -0.8157004     -0.7257079     -0.8095509 
##   hsa-mir-513b   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3 
##     -0.6391351     -0.6802698     -0.7502505     -0.7560365     -0.7577167 
##   hsa-mir-514b    hsa-mir-543    hsa-mir-544    hsa-mir-582    hsa-mir-615 
##     -0.6915826     -0.3114163     -0.2319221      0.2220790      0.2358871 
##    hsa-mir-655    hsa-mir-668    hsa-mir-887    hsa-mir-889    hsa-mir-92b 
##     -0.2241513     -0.2524937      0.2244516     -0.1886266      0.2053577 
##     hsa-mir-96 
##      0.2137223 
## 
## $`5f`$Factor4
## PEA15.RPPA 
##  0.1940685 
## 
## $`5f`$Factor5
## PARP1.R2Gn 
##  0.1860451 
## 
## 
## $`10f`
## $`10f`$Factor1
##  hsa-mir-101-2   hsa-mir-1258    hsa-mir-139   hsa-mir-146a    hsa-mir-150 
##      0.1629177      0.1454717     -0.1527660      0.2439511      0.2176340 
## hsa-mir-196a-1 hsa-mir-196a-2    hsa-mir-210  hsa-mir-218-2   hsa-mir-301b 
##     -0.1894599     -0.1409968     -0.1544269     -0.1662055     -0.1581296 
##   hsa-mir-3065    hsa-mir-362   hsa-mir-378c   hsa-mir-3940    hsa-mir-488 
##     -0.1475613      0.2013512      0.1418129     -0.1491676     -0.1499323 
##    hsa-mir-510    hsa-mir-605    hsa-mir-653    hsa-mir-887    hsa-mir-9-1 
##      0.1519868      0.1691677      0.2167146     -0.1459726     -0.1492127 
##    hsa-mir-9-2     hsa-mir-95    hsa-mir-99a      CDH2.R2Gn      FASN.R2Gn 
##     -0.1498007     -0.1506946      0.1655920     -0.1476591     -0.1960203 
##     PRKCA.R2Gn      ANLN.R2Gn     STMN1.R2Gn    RAB11A.R2Gn      ETS1.R2Gn 
##      0.1897229     -0.1483475     -0.2373242     -0.1625782      0.1555535 
##      CDK1.R2Gn    CTNNA1.R2Gn      TYMS.R2Gn      MSH6.R2Gn     CCNB1.R2Gn 
##     -0.2289052      0.2068288     -0.1729913     -0.1780294     -0.2314913 
##      PDK1.R2Gn     FOXM1.R2Gn    COL6A1.R2Gn    STAT5A.R2Gn     YWHAB.R2Gn 
##     -0.1450866     -0.1603136      0.1483476      0.1690133      0.1658905 
##     ANXA1.R2Gn     PREX1.R2Gn    SQSTM1.R2Gn      G6PD.RPPA    IGFBP2.RPPA 
##      0.1529496      0.1735357      0.1430024      0.4649610     -0.2495660 
##      ASNS.RPPA     RBM15.RPPA     GATA3.RPPA     PEA15.RPPA       ATM.RPPA 
##      0.1845150     -0.7031606      0.4185162     -0.1961371     -0.2976696 
##     BRCA2.RPPA      FASN.RPPA    INPP4B.RPPA    ACVRL1.RPPA      TSC1.RPPA 
##      0.2778099     -1.1854465      0.4445420      0.1634472     -0.3088216 
##      TTF1.RPPA      CDK1.RPPA       VHL.RPPA        AR.RPPA     PRDX1.RPPA 
##      0.3018635      0.3171725      0.5434133      0.1688745      0.5653009 
##      XBP1.RPPA     GAPDH.RPPA      MSH6.RPPA     MYH11.RPPA      PDK1.RPPA 
##      0.3994834     -0.5204806     -0.8080000      0.2798145      0.1510109 
##      TFRC.RPPA      MSH2.RPPA     PREX1.RPPA 
##     -0.4650862     -0.2984680      0.5079902 
## 
## $`10f`$Factor2
##    hsa-mir-100  hsa-mir-105-2 hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1193 
##      0.1667214      0.1476208     -0.7757787     -0.7684686     -0.6118972 
##   hsa-mir-1197   hsa-mir-1224   hsa-mir-1245   hsa-mir-1247   hsa-mir-1251 
##     -0.8106640      0.1649559      0.1708265      0.1578687      0.1508070 
##   hsa-mir-1258    hsa-mir-127 hsa-mir-1270-2  hsa-mir-129-2   hsa-mir-1291 
##      0.2967204     -0.6143032     -0.1482040      0.2151572      0.1911404 
##    hsa-mir-134 hsa-mir-135a-1    hsa-mir-136    hsa-mir-137  hsa-mir-138-1 
##     -0.5639862      0.2104407     -0.6320459      0.3159860      0.2708478 
##  hsa-mir-138-2    hsa-mir-154   hsa-mir-1909    hsa-mir-204    hsa-mir-205 
##      0.1934429     -0.6310229     -0.1482276      0.1670878      0.2006872 
##    hsa-mir-206   hsa-mir-2114    hsa-mir-299   hsa-mir-3193    hsa-mir-323 
##      0.1796628      0.1568462     -0.6040230      0.1416263     -0.7222756 
##   hsa-mir-323b  hsa-mir-329-1  hsa-mir-329-2    hsa-mir-337    hsa-mir-33b 
##     -0.7419769     -0.9263064     -0.6799496     -0.4582561      0.1917758 
##    hsa-mir-34b    hsa-mir-369    hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2 
##      0.1495366     -0.5849407     -0.6314871     -0.6638160     -0.6738463 
##   hsa-mir-376b   hsa-mir-376c    hsa-mir-377    hsa-mir-379    hsa-mir-380 
##     -0.6039874     -0.5940351     -0.6003941     -0.5850655     -0.7232468 
##    hsa-mir-381    hsa-mir-382    hsa-mir-383   hsa-mir-3909   hsa-mir-3922 
##     -0.5862670     -0.6325155     -0.1731483      0.1873861      0.1956569 
##   hsa-mir-3934    hsa-mir-409    hsa-mir-410    hsa-mir-411    hsa-mir-412 
##      0.1405914     -0.6230285     -0.6622328     -0.7261397     -0.5606990 
##    hsa-mir-431    hsa-mir-432    hsa-mir-433    hsa-mir-466    hsa-mir-485 
##     -0.6425268     -0.6511705     -0.6874613      0.4145631     -0.6997358 
##   hsa-mir-487a   hsa-mir-487b    hsa-mir-488    hsa-mir-489    hsa-mir-490 
##     -0.7420009     -0.6732689      0.2419606      0.2291096      0.2628658 
##    hsa-mir-493    hsa-mir-494    hsa-mir-495    hsa-mir-496    hsa-mir-499 
##     -0.5468529     -0.6323493     -0.5617642     -0.6429590      0.2313994 
##    hsa-mir-506    hsa-mir-507    hsa-mir-508  hsa-mir-509-1  hsa-mir-509-2 
##      0.3096959      0.3055074      0.2930038      0.2866548      0.2849193 
##  hsa-mir-509-3    hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2   hsa-mir-513b 
##      0.2869746      0.3737925      0.2657331      0.3251164      0.2889396 
##   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2  hsa-mir-514-3   hsa-mir-514b 
##      0.3184157      0.2776071      0.2795785      0.2788993      0.2689486 
##   hsa-mir-517a   hsa-mir-518b   hsa-mir-518f   hsa-mir-520a   hsa-mir-526b 
##      0.2644774      0.1626558      0.1716351      0.2239893      0.2047622 
##    hsa-mir-539    hsa-mir-541    hsa-mir-543    hsa-mir-544   hsa-mir-548s 
##     -0.6406990     -0.6928630     -0.6504994     -0.3885738      0.1430110 
##   hsa-mir-548v hsa-mir-550a-2    hsa-mir-577    hsa-mir-585    hsa-mir-605 
##      0.1809890      0.1542264      0.2681238      0.2737091      0.2267991 
##    hsa-mir-639    hsa-mir-653    hsa-mir-654    hsa-mir-655    hsa-mir-656 
##      0.1789042      0.1557767     -0.5932516     -0.7303706     -0.7603929 
##    hsa-mir-665    hsa-mir-668    hsa-mir-676    hsa-mir-758    hsa-mir-767 
##     -0.6939368     -0.8925683      0.1587216     -0.5663007      0.1807970 
##    hsa-mir-770    hsa-mir-889   hsa-mir-891a     hsa-mir-95 
##     -0.7861210     -0.6554383      0.1917885      0.1398462 
## 
## $`10f`$Factor3
##   G6PD.RPPA IGFBP2.RPPA  RBM15.RPPA   PTEN.RPPA  GATA3.RPPA  PEA15.RPPA 
##   0.3529247   0.2235950  -0.3091065  -0.4563414   0.1400799  -0.2244356 
##    ATM.RPPA   EGFR.RPPA INPP4B.RPPA ACVRL1.RPPA   TSC1.RPPA  PDCD4.RPPA 
##  -0.2509778  -0.1518510   0.2045552   0.1401543  -0.1826618  -0.4109748 
##   CDK1.RPPA    VHL.RPPA  PRDX1.RPPA   XBP1.RPPA  ERCC1.RPPA   TFRC.RPPA 
##   0.1680966   0.2265389   0.2595026   0.2400194  -0.1476577  -0.1788825 
##  PREX1.RPPA 
##   0.2135643 
## 
## $`10f`$Factor4
## hsa-mir-1185-1 hsa-mir-1185-2   hsa-mir-1197   hsa-mir-1224   hsa-mir-1226 
##     -0.1899032     -0.1406181     -0.1567997     -0.1622436      0.2013880 
##   hsa-mir-1229  hsa-mir-124-3   hsa-mir-1249  hsa-mir-1255a   hsa-mir-1258 
##      0.1627852      0.1972792      0.2013092      0.1628381     -0.3447852 
##   hsa-mir-1291   hsa-mir-1292   hsa-mir-135b    hsa-mir-139    hsa-mir-182 
##     -0.1428185      0.1776674      0.2185706      0.2925311      0.2095041 
##    hsa-mir-183    hsa-mir-184    hsa-mir-187 hsa-mir-196a-1 hsa-mir-196a-2 
##      0.2128228     -0.2045339      0.1699140      0.1975691      0.1904193 
##   hsa-mir-196b    hsa-mir-206    hsa-mir-210   hsa-mir-2114   hsa-mir-216b 
##      0.2097269      0.1561514     -0.1582593     -0.2516953     -0.1971690 
##  hsa-mir-218-1  hsa-mir-218-2   hsa-mir-3166   hsa-mir-3170   hsa-mir-3190 
##      0.1833000      0.2043498      0.2622004      0.2178932      0.1418359 
## hsa-mir-3199-1   hsa-mir-323b    hsa-mir-338   hsa-mir-3605   hsa-mir-3655 
##     -0.1625380     -0.1555429      0.1969098      0.1488437     -0.2656059 
##   hsa-mir-3690 hsa-mir-376a-2    hsa-mir-383   hsa-mir-3917   hsa-mir-3923 
##     -0.1430867     -0.2118430      0.1994986      0.1702260      0.2342099 
## hsa-mir-3926-2    hsa-mir-411    hsa-mir-466    hsa-mir-485   hsa-mir-487a 
##     -0.1606206     -0.1949755     -0.1413170     -0.2529788     -0.1521015 
##    hsa-mir-494    hsa-mir-506    hsa-mir-507    hsa-mir-508  hsa-mir-509-1 
##     -0.1615179     -0.6782678     -0.7587051     -0.6876708     -0.6887159 
##  hsa-mir-509-2  hsa-mir-509-3    hsa-mir-510  hsa-mir-511-2 hsa-mir-513a-1 
##     -0.6844518     -0.6827294     -0.8044964     -0.1585291     -0.6867524 
## hsa-mir-513a-2   hsa-mir-513b   hsa-mir-513c  hsa-mir-514-1  hsa-mir-514-2 
##     -0.7446260     -0.6228126     -0.6547784     -0.6779802     -0.6837980 
##  hsa-mir-514-3   hsa-mir-514b    hsa-mir-543    hsa-mir-544    hsa-mir-582 
##     -0.6835320     -0.6983735     -0.2354951     -0.1853546      0.2105771 
##    hsa-mir-615    hsa-mir-668    hsa-mir-760    hsa-mir-876    hsa-mir-887 
##      0.2115752     -0.1888667      0.1482735     -0.1476502      0.1912648 
##    hsa-mir-92b     hsa-mir-96 
##      0.2082682      0.1794035 
## 
## $`10f`$Factor5
## IGFBP2.RPPA  RBM15.RPPA   EGFR.RPPA   TSC1.RPPA  GAPDH.RPPA  ERCC1.RPPA 
##   0.1432934   0.1444952  -0.1754455   0.1546405  -0.1664315  -0.1930599 
## 
## $`10f`$Factor6
##  G6PD.RPPA  ASNS.RPPA RBM15.RPPA GATA3.RPPA  EGFR.RPPA GAPDH.RPPA PREX1.RPPA 
##  0.1433544  0.1942848 -0.2828889 -0.1858416  0.1668751  0.1652671 -0.2089479 
## 
## $`10f`$Factor7
##  ANLN.R2Gn STMN1.R2Gn  CDK1.R2Gn CCNB1.R2Gn FOXM1.R2Gn 
##  0.2266988  0.2299727  0.2035736  0.2148030  0.1838917 
## 
## $`10f`$Factor8
## named numeric(0)
## 
## $`10f`$Factor9
## named numeric(0)
## 
## $`10f`$Factor10
## named numeric(0)

1. Convert microRNA to genes

Also remove the ending “.R2Gn” and “.RPPA” from gene names.

split.by.omic = function(variable.list) {
  out.mRSG = variable.list[startsWith(variable.list, "hsa")]
  out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
  out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
  out = list("miRNASeqGene" = out.mRSG,
             "RNASeq2GeneNorm" = out.R2Gn,
             "RPPAArray" = out.RPPA)
  out
}
multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
  multiomics.list = split.by.omic(sel.features)
  # Convert miRNASeqGene to target GENE names
  # Skipped and returns an empty list instead of the list of select features,
  # or if microRNA features are explicitly dropped (drop.miRNA = T).
  # (Usually done when the features has only a few miRNA and unable to target any genes)
  if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
    if (!full.search) { # Search only among the 198 genes in ACC, recommended
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          target = gene.names,
                          table = table,
                          summary = T)
    mRSG.target.genes = unique(targets@data$target_symbol)
    } else { # Search the full dataset, not recommended. 
             # Use only if ACC gene search returns nothing or fails.
             # Genes not in the ACC genes need to be manually removed.
    targets= get_multimir(mirna = multiomics.list[[1]], 
                          table = table,
                          summary = T)  
    mRSG.target.genes = unique(targets@data$target_symbol)
    }
    
  } else {
    mRSG.target.genes = list()
  }
  #Remove suffix for Pathway Analysis Compatibility
  R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
  
  RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
  
  #Join all cleaned-up genes are remove duplicates.
  out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes)
  out = as.character(unique(out1))
  out
}
geneNames <- list("Factor1of1"= multiomics.to.GENES(names(sel.features$`1f`$Factor1)),
                  
                  "Factor1of2"= multiomics.to.GENES(names(sel.features$`2f`$Factor1)),
                  "Factor2of2"= multiomics.to.GENES(names(sel.features$`2f`$Factor2)),
                  
                  "Factor1of3"= multiomics.to.GENES(names(sel.features$`3f`$Factor1)),
                  "Factor2of3"= multiomics.to.GENES(names(sel.features$`3f`$Factor2)),
                  "Factor3of3"= multiomics.to.GENES(names(sel.features$`3f`$Factor3)), # Empty
                  
                  "Factor1of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor1)),
                  "Factor2of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor2)),
                  "Factor3of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor3)),
                  "Factor4of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor4)),
                  "Factor5of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor5)),
                  
                  "Factor1of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor1)),
                  "Factor2of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor2)),
                  "Factor3of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor3)),
                  "Factor4of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor4)),
                  "Factor5of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor5)),
                  "Factor6of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor6)),
                  "Factor7of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor7)),
                  "Factor8of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor8)), # Empty
                  "Factor9of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor9)), # Empty
                  "Factor10of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor10)) # Empty
                  )
## Searching mirecords ...
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geneNames
## $Factor1of1
##  [1] "HSPA1A"  "AKT1"    "VHL"     "MTOR"    "MAPK8"   "MYH9"    "CDKN1A" 
##  [8] "FOXO3"   "ATM"     "CASP8"   "MACC1"   "PTEN"    "KRAS"    "NRAS"   
## [15] "PTK2"    "ETS1"    "CCND1"   "PIK3R1"  "XIAP"    "CHEK1"   "IGF1R"  
## [22] "SRSF1"   "TUBA1B"  "STAT5A"  "KIT"     "NCOA3"   "EGFR"    "EZH2"   
## [29] "PTGS2"   "MET"     "AKT2"    "YBX1"    "PRKAA1"  "PXN"     "AXL"    
## [36] "MSH2"    "CASP3"   "CCNE1"   "YAP1"    "EIF4E"   "EIF4G1"  "GAPDH"  
## [43] "ITGA2"   "PRKCA"   "MAPK1"   "TFRC"    "YWHAE"   "RAB11A"  "ANLN"   
## [50] "RICTOR"  "TP53BP1" "BRAF"   
## 
## $Factor1of2
##  [1] "RB1"    "XIAP"   "CTNNA1" "G6PD"   "IGFBP2" "RBM15"  "ATM"    "FASN"  
##  [9] "INPP4B" "TSC1"   "TTF1"   "VHL"    "PRDX1"  "XBP1"   "MSH6"   "TFRC"  
## [17] "MSH2"   "PREX1" 
## 
## $Factor2of2
##  [1] "HSPA1A"  "AKT1"    "VHL"     "MTOR"    "MAPK8"   "MYH9"    "CDKN1A" 
##  [8] "FOXO3"   "ATM"     "CASP8"   "MACC1"   "PTEN"    "KRAS"    "NRAS"   
## [15] "PTK2"    "ETS1"    "PARP1"   "IGF1R"   "CCNE2"   "RAB25"   "CCND1"  
## [22] "PIK3R1"  "XIAP"    "CHEK1"   "SRSF1"   "TUBA1B"  "STAT5A"  "KIT"    
## [29] "NCOA3"   "EGFR"    "EZH2"    "PTGS2"   "MET"     "AKT2"    "YBX1"   
## [36] "PRKAA1"  "PXN"     "BCL2"    "AXL"     "MYC"     "MSH2"    "CASP3"  
## [43] "BCL2L11" "CCNE1"   "YAP1"    "EIF4E"   "EIF4G1"  "GAPDH"   "MSH6"   
## [50] "ITGA2"   "PIK3CA"  "PRKCA"   "MAPK1"   "TFRC"    "YWHAE"   "RAB11A" 
## [57] "ANLN"    "RICTOR"  "TP53BP1" "BRAF"   
## 
## $Factor1of3
##  [1] "RB1"     "XIAP"    "HSPA1A"  "AKT1"    "VHL"     "MTOR"    "MAPK8"  
##  [8] "ETS1"    "ARID1A"  "BID"     "MYH9"    "CDKN1A"  "FOXO3"   "ATM"    
## [15] "CASP8"   "MACC1"   "PTEN"    "KRAS"    "NRAS"    "PTK2"    "PARP1"  
## [22] "IGF1R"   "CCNE2"   "RAB25"   "CCND1"   "PIK3R1"  "CHEK1"   "SRSF1"  
## [29] "TUBA1B"  "STAT5A"  "KIT"     "NCOA3"   "EGFR"    "EZH2"    "PTGS2"  
## [36] "MET"     "AKT2"    "YBX1"    "PRKAA1"  "PXN"     "BCL2"    "AXL"    
## [43] "MYC"     "MSH2"    "CASP3"   "BCL2L11" "CCNE1"   "YAP1"    "EIF4E"  
## [50] "EIF4G1"  "GAPDH"   "MSH6"    "ITGA2"   "PIK3CA"  "PRKCA"   "MAPK1"  
## [57] "TFRC"    "YWHAE"   "RAB11A"  "GAB2"    "ANLN"    "RICTOR"  "TP53BP1"
## [64] "BRAF"    "G6PD"    "FASN"    "INPP4B"  "PRDX1"  
## 
## $Factor2of3
##  [1] "AKT2"   "BCL2"   "MYC"    "AKT1"   "BCL2L1" "RB1"    "XIAP"   "ETS1"  
##  [9] "MAPK8"  "ARID1A" "BID"    "PTEN"   "KRAS"   "NRAS"   "PTK2"   "ATM"   
## [17] "YWHAZ"  "CCND1"  "CDKN1A" "NF2"    "NCOA3"  "ITGA2"  "GAB2"   "RBM15" 
## [25] "TSC1"   "TTF1"   "VHL"    "PREX1" 
## 
## $Factor3of3
## character(0)
## 
## $Factor1of5
##  [1] "STMN1"  "CDK1"   "CCNB1"  "G6PD"   "IGFBP2" "RBM15"  "GATA3"  "ATM"   
##  [9] "BRCA2"  "FASN"   "INPP4B" "TSC1"   "TTF1"   "VHL"    "PRDX1"  "XBP1"  
## [17] "GAPDH"  "MSH6"   "MYH11"  "TFRC"   "MSH2"   "PREX1" 
## 
## $Factor2of5
##  [1] "RB1"     "XIAP"    "HSPA1A"  "AKT1"    "VHL"     "MTOR"    "MAPK8"  
##  [8] "ETS1"    "ARID1A"  "BID"     "MYH9"    "CDKN1A"  "FOXO3"   "ATM"    
## [15] "CASP8"   "MACC1"   "PTEN"    "KRAS"    "NRAS"    "PTK2"    "PARP1"  
## [22] "IGF1R"   "CCNE2"   "RAB25"   "CCND1"   "PIK3R1"  "CHEK1"   "SRSF1"  
## [29] "TUBA1B"  "STAT5A"  "KIT"     "NCOA3"   "EGFR"    "EZH2"    "PTGS2"  
## [36] "MET"     "AKT2"    "YBX1"    "PRKAA1"  "PXN"     "BCL2"    "E2F1"   
## [43] "CASP9"   "AXL"     "CDKN2A"  "MYC"     "MSH2"    "CASP3"   "BCL2L11"
## [50] "CCNE1"   "MAPK9"   "RAF1"    "YAP1"    "BCL2L1"  "DVL3"    "EIF4E"  
## [57] "EIF4G1"  "GAPDH"   "MSH6"    "ITGA2"   "SMAD3"   "PIK3CA"  "PRKCA"  
## [64] "MAPK1"   "MAPK3"   "TFRC"    "YWHAE"   "RAB11A"  "GAB2"    "ANLN"   
## [71] "RICTOR"  "TP53BP1" "BRAF"   
## 
## $Factor3of5
##  [1] "ESR1"   "MET"    "AKT2"   "G6PD"   "BCL2"   "KRAS"   "CCND1"  "NOTCH3"
##  [9] "AKT1"   "IGF1R"  "MYC"    "BCL2L1" "RB1"    "XIAP"   "ETS1"   "MAPK8" 
## [17] "ARID1A" "BID"    "PTEN"   "NRAS"   "PTK2"   "ATM"    "YWHAZ"  "ITGA2" 
## [25] "MAPK1"  "PXN"    "YWHAB"  "CDKN1A" "STAT5A" "NF2"    "NCOA3"  "FOXO3" 
## [33] "CHEK1"  "FN1"    "XRCC1"  "GAB2"  
## 
## $Factor4of5
## [1] "PEA15"
## 
## $Factor5of5
## [1] "PARP1"
## 
## $Factor1of10
##  [1] "RB1"     "XIAP"    "AKT1"    "ACACA"   "PTEN"    "BCL2"    "BCL2L11"
##  [8] "PARP1"   "CTNNA1"  "EEF2"    "GATA3"   "NRG1"    "IGF1R"   "MAPK1"  
## [15] "TFRC"    "NDRG1"   "AKT1S1"  "RICTOR"  "TP53BP1" "GSK3A"   "CDH2"   
## [22] "FASN"    "PRKCA"   "ANLN"    "STMN1"   "RAB11A"  "ETS1"    "CDK1"   
## [29] "TYMS"    "MSH6"    "CCNB1"   "PDK1"    "FOXM1"   "COL6A1"  "STAT5A" 
## [36] "YWHAB"   "ANXA1"   "PREX1"   "SQSTM1"  "G6PD"    "IGFBP2"  "ASNS"   
## [43] "RBM15"   "PEA15"   "ATM"     "BRCA2"   "INPP4B"  "ACVRL1"  "TSC1"   
## [50] "TTF1"    "VHL"     "AR"      "PRDX1"   "XBP1"    "GAPDH"   "MYH11"  
## [57] "MSH2"   
## 
## $Factor2of10
##  [1] "ESR1"    "MET"     "G6PD"    "BCL2"    "KRAS"    "CCND1"   "NOTCH3" 
##  [8] "AKT1"    "IGF1R"   "RB1"     "XIAP"    "CDKN1A"  "HSPA1A"  "VHL"    
## [15] "MTOR"    "MAPK8"   "ETS1"    "ARID1A"  "BID"     "MYH9"    "FOXO3"  
## [22] "ATM"     "CASP8"   "MACC1"   "PTEN"    "NRAS"    "PTK2"    "PARP1"  
## [29] "CCNE2"   "RAB25"   "AR"      "EIF4E"   "MAPT"    "RAD51"   "ERCC1"  
## [36] "PIK3R1"  "CHEK1"   "SRSF1"   "TUBA1B"  "STAT5A"  "CDKN1B"  "BCL2L11"
## [43] "KIT"     "NCOA3"   "EGFR"    "EZH2"    "PTGS2"   "AKT2"    "YBX1"   
## [50] "PRKAA1"  "PXN"     "E2F1"    "CASP9"   "AXL"     "CDKN2A"  "MYC"    
## [57] "MSH2"    "CASP3"   "CCNE1"   "MAPK9"   "RAF1"    "YAP1"    "BCL2L1" 
## [64] "DVL3"    "EIF4G1"  "FN1"     "GAPDH"   "MSH6"    "ITGA2"   "SMAD3"  
## [71] "SMAD4"   "PIK3CA"  "PRKCA"   "MAPK1"   "MAPK3"   "TFRC"    "YWHAE"  
## [78] "RAB11A"  "GAB2"    "ANLN"    "RICTOR"  "TP53BP1" "BRAF"   
## 
## $Factor3of10
##  [1] "G6PD"   "IGFBP2" "RBM15"  "PTEN"   "GATA3"  "PEA15"  "ATM"    "EGFR"  
##  [9] "INPP4B" "ACVRL1" "TSC1"   "PDCD4"  "CDK1"   "VHL"    "PRDX1"  "XBP1"  
## [17] "ERCC1"  "TFRC"   "PREX1" 
## 
## $Factor4of10
##  [1] "ESR1"   "MET"    "AKT2"   "G6PD"   "BCL2"   "KRAS"   "CCND1"  "NOTCH3"
##  [9] "AKT1"   "IGF1R"  "MYC"    "BCL2L1" "RB1"    "XIAP"   "TUBA1B" "ETS1"  
## [17] "MAPK8"  "ARID1A" "BID"    "PTEN"   "NRAS"   "PTK2"   "ATM"    "YWHAZ" 
## [25] "ITGA2"  "MAPK1"  "PXN"    "YWHAB"  "PIK3R1" "CHEK1"  "SRSF1"  "CDKN1A"
## [33] "STAT5A" "RAF1"   "PRKAA1" "ACACA"  "NF2"    "NCOA3"  "E2F1"   "CASP9" 
## [41] "AXL"    "CDKN2A" "CCNE1"  "MAPK9"  "FOXO3"  "CTNNB1" "DVL3"   "FN1"   
## [49] "SMAD3"  "PRKCA"  "MAPK3"  "XRCC1"  "GAB2"   "WWTR1"  "TSC2"  
## 
## $Factor5of10
## [1] "IGFBP2" "RBM15"  "EGFR"   "TSC1"   "GAPDH"  "ERCC1" 
## 
## $Factor6of10
## [1] "G6PD"  "ASNS"  "RBM15" "GATA3" "EGFR"  "GAPDH" "PREX1"
## 
## $Factor7of10
## [1] "ANLN"  "STMN1" "CDK1"  "CCNB1" "FOXM1"
## 
## $Factor8of10
## character(0)
## 
## $Factor9of10
## character(0)
## 
## $Factor10of10
## character(0)
saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_mofa_extracted_by_bic.rds")

2. Pathway Analysis

A. GO Classification

ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]

  ggo_MF[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="MF",
    keyType="SYMBOL",
    readable=TRUE)
  
  ggo_BP[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="BP",
    keyType="SYMBOL",
    readable=TRUE)

  ggo_CC[[z]] <- groupGO(gene=input,
    OrgDb = org.Hs.eg.db,
    ont="CC",
    keyType="SYMBOL",
    readable=TRUE)    
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19
## [1] 20
## [1] 21
for(z in 1:length(geneNames)) {
  print(head(ggo_MF[[z]]))
  print(head(ggo_BP[[z]]))
  print(head(ggo_CC[[z]]))
}
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/52
## GO:0003824 GO:0003824           catalytic activity    35     35/52
## GO:0005198 GO:0005198 structural molecule activity     1      1/52
## GO:0005215 GO:0005215         transporter activity     1      1/52
## GO:0005488 GO:0005488                      binding    52     52/52
## GO:0009055 GO:0009055   electron transfer activity     0      0/52
##                                                                                                                                                                                                                                                                                                          geneID
## GO:0003774                                                                                                                                                                                                                                                                                                 MYH9
## GO:0003824                                                                                                    HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/PIK3R1/XIAP/CHEK1/IGF1R/TUBA1B/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/PRKAA1/AXL/MSH2/CASP3/CCNE1/GAPDH/PRKCA/MAPK1/RAB11A/BRAF
## GO:0005198                                                                                                                                                                                                                                                                                               TUBA1B
## GO:0005215                                                                                                                                                                                                                                                                                                IGF1R
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/AXL/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/ITGA2/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/ANLN/RICTOR/TP53BP1/BRAF
## GO:0009055                                                                                                                                                                                                                                                                                                     
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    16     16/52
## GO:0002376 GO:0002376 immune system process    27     27/52
## GO:0008152 GO:0008152     metabolic process    47     47/52
## GO:0009987 GO:0009987      cellular process    52     52/52
## GO:0016032 GO:0016032         viral process     6      6/52
## GO:0022414 GO:0022414  reproductive process    16     16/52
##                                                                                                                                                                                                                                                                                                          geneID
## GO:0000003                                                                                                                                                                                                                  AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/IGF1R/KIT/EGFR/PTGS2/AXL/MSH2/CASP3/CCNE1/ITGA2
## GO:0002376                                                                                                                                               HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/PIK3R1/XIAP/IGF1R/KIT/EZH2/AXL/MSH2/CASP3/GAPDH/ITGA2/PRKCA/MAPK1/TFRC/YWHAE/TP53BP1/BRAF
## GO:0008152                             HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/AXL/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/ITGA2/PRKCA/MAPK1/TFRC/YWHAE/RICTOR/TP53BP1/BRAF
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/AXL/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/ITGA2/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/ANLN/RICTOR/TP53BP1/BRAF
## GO:0016032                                                                                                                                                                                                                                                                      HSPA1A/AKT1/EGFR/AXL/ITGA2/TFRC
## GO:0022414                                                                                                                                                                                                                  AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/IGF1R/KIT/EGFR/PTGS2/AXL/MSH2/CASP3/CCNE1/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    38     38/52
## GO:0044423 GO:0044423           virion component     0      0/52
## GO:0110165 GO:0110165 cellular anatomical entity    52     52/52
##                                                                                                                                                                                                                                                                                                          geneID
## GO:0032991                                                                            HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/CCND1/PIK3R1/CHEK1/IGF1R/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/YBX1/PRKAA1/PXN/AXL/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/ITGA2/PRKCA/TFRC/RAB11A/RICTOR/TP53BP1
## GO:0044423                                                                                                                                                                                                                                                                                                     
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/PIK3R1/XIAP/CHEK1/IGF1R/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/AXL/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/ITGA2/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/ANLN/RICTOR/TP53BP1/BRAF
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/18
## GO:0003824 GO:0003824           catalytic activity     9      9/18
## GO:0005198 GO:0005198 structural molecule activity     1      1/18
## GO:0005215 GO:0005215         transporter activity     0      0/18
## GO:0005488 GO:0005488                      binding    18     18/18
## GO:0009055 GO:0009055   electron transfer activity     0      0/18
##                                                                                                     geneID
## GO:0003774                                                                                                
## GO:0003824                                                   XIAP/G6PD/ATM/FASN/INPP4B/VHL/PRDX1/MSH6/MSH2
## GO:0005198                                                                                          CTNNA1
## GO:0005215                                                                                                
## GO:0005488 RB1/XIAP/CTNNA1/G6PD/IGFBP2/RBM15/ATM/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/MSH6/TFRC/MSH2/PREX1
## GO:0009055                                                                                                
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     6      6/18
## GO:0002376 GO:0002376 immune system process    13     13/18
## GO:0008152 GO:0008152     metabolic process    16     16/18
## GO:0009987 GO:0009987      cellular process    18     18/18
## GO:0016032 GO:0016032         viral process     1      1/18
## GO:0022414 GO:0022414  reproductive process     6      6/18
##                                                                                                     geneID
## GO:0000003                                                                 RB1/CTNNA1/IGFBP2/ATM/MSH6/MSH2
## GO:0002376                             RB1/XIAP/G6PD/IGFBP2/RBM15/ATM/TSC1/PRDX1/XBP1/MSH6/TFRC/MSH2/PREX1
## GO:0008152               RB1/XIAP/G6PD/RBM15/ATM/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/MSH6/TFRC/MSH2/PREX1
## GO:0009987 RB1/XIAP/CTNNA1/G6PD/IGFBP2/RBM15/ATM/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/MSH6/TFRC/MSH2/PREX1
## GO:0016032                                                                                            TFRC
## GO:0022414                                                                 RB1/CTNNA1/IGFBP2/ATM/MSH6/MSH2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     9      9/18
## GO:0044423 GO:0044423           virion component     0      0/18
## GO:0110165 GO:0110165 cellular anatomical entity    18     18/18
##                                                                                                     geneID
## GO:0032991                                                   RB1/CTNNA1/RBM15/ATM/TSC1/XBP1/MSH6/TFRC/MSH2
## GO:0044423                                                                                                
## GO:0110165 RB1/XIAP/CTNNA1/G6PD/IGFBP2/RBM15/ATM/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/MSH6/TFRC/MSH2/PREX1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/60
## GO:0003824 GO:0003824           catalytic activity    39     39/60
## GO:0005198 GO:0005198 structural molecule activity     1      1/60
## GO:0005215 GO:0005215         transporter activity     2      2/60
## GO:0005488 GO:0005488                      binding    60     60/60
## GO:0009055 GO:0009055   electron transfer activity     0      0/60
##                                                                                                                                                                                                                                                                                                                                                         geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                                MYH9
## GO:0003824                                                                                                                           HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/RAB25/CCND1/PIK3R1/XIAP/CHEK1/TUBA1B/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/PRKAA1/AXL/MSH2/CASP3/CCNE1/GAPDH/MSH6/PIK3CA/PRKCA/MAPK1/RAB11A/BRAF
## GO:0005198                                                                                                                                                                                                                                                                                                                                              TUBA1B
## GO:0005215                                                                                                                                                                                                                                                                                                                                          IGF1R/BCL2
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/XIAP/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/ANLN/RICTOR/TP53BP1/BRAF
## GO:0009055                                                                                                                                                                                                                                                                                                                                                    
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    22     22/60
## GO:0002376 GO:0002376 immune system process    33     33/60
## GO:0008152 GO:0008152     metabolic process    53     53/60
## GO:0009987 GO:0009987      cellular process    60     60/60
## GO:0016032 GO:0016032         viral process     7      7/60
## GO:0022414 GO:0022414  reproductive process    22     22/60
##                                                                                                                                                                                                                                                                                                                                                         geneID
## GO:0000003                                                                                                                                                                                                                            AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/KIT/EGFR/PTGS2/BCL2/AXL/MSH2/CASP3/BCL2L11/CCNE1/MSH6/ITGA2/PIK3CA
## GO:0002376                                                                                                                                                           HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/PARP1/IGF1R/PIK3R1/XIAP/KIT/EZH2/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/TP53BP1/BRAF
## GO:0008152                                           HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/XIAP/CHEK1/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/BCL2/AXL/MYC/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RICTOR/TP53BP1/BRAF
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/XIAP/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/ANLN/RICTOR/TP53BP1/BRAF
## GO:0016032                                                                                                                                                                                                                                                                                                                HSPA1A/AKT1/EGFR/BCL2/AXL/ITGA2/TFRC
## GO:0022414                                                                                                                                                                                                                            AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/KIT/EGFR/PTGS2/BCL2/AXL/MSH2/CASP3/BCL2L11/CCNE1/MSH6/ITGA2/PIK3CA
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    45     45/60
## GO:0044423 GO:0044423           virion component     0      0/60
## GO:0110165 GO:0110165 cellular anatomical entity    60     60/60
##                                                                                                                                                                                                                                                                                                                                                         geneID
## GO:0032991                                                                                  HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/CHEK1/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/TFRC/RAB11A/RICTOR/TP53BP1
## GO:0044423                                                                                                                                                                                                                                                                                                                                                    
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/XIAP/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/ANLN/RICTOR/TP53BP1/BRAF
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/68
## GO:0003824 GO:0003824           catalytic activity    43     43/68
## GO:0005198 GO:0005198 structural molecule activity     1      1/68
## GO:0005215 GO:0005215         transporter activity     2      2/68
## GO:0005488 GO:0005488                      binding    68     68/68
## GO:0009055 GO:0009055   electron transfer activity     0      0/68
##                                                                                                                                                                                                                                                                                                                                                                                                    geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                                                                           MYH9
## GO:0003824                                                                                                                                               XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/RAB25/CCND1/PIK3R1/CHEK1/TUBA1B/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/PRKAA1/AXL/MSH2/CASP3/CCNE1/GAPDH/MSH6/PIK3CA/PRKCA/MAPK1/RAB11A/BRAF/G6PD/FASN/INPP4B/PRDX1
## GO:0005198                                                                                                                                                                                                                                                                                                                                                                                         TUBA1B
## GO:0005215                                                                                                                                                                                                                                                                                                                                                                                     IGF1R/BCL2
## GO:0005488 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF/G6PD/FASN/INPP4B/PRDX1
## GO:0009055                                                                                                                                                                                                                                                                                                                                                                                               
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    23     23/68
## GO:0002376 GO:0002376 immune system process    39     39/68
## GO:0008152 GO:0008152     metabolic process    60     60/68
## GO:0009987 GO:0009987      cellular process    68     68/68
## GO:0016032 GO:0016032         viral process     7      7/68
## GO:0022414 GO:0022414  reproductive process    23     23/68
##                                                                                                                                                                                                                                                                                                                                                                                                    geneID
## GO:0000003                                                                                                                                                                                                                                                                   RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/KIT/EGFR/PTGS2/BCL2/AXL/MSH2/CASP3/BCL2L11/CCNE1/MSH6/ITGA2/PIK3CA
## GO:0002376                                                                                                                                                                       RB1/XIAP/HSPA1A/AKT1/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/PARP1/IGF1R/PIK3R1/KIT/EZH2/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/GAB2/TP53BP1/BRAF/G6PD/PRDX1
## GO:0008152                                                RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/CHEK1/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/BCL2/AXL/MYC/MSH2/CASP3/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RICTOR/TP53BP1/BRAF/G6PD/FASN/INPP4B/PRDX1
## GO:0009987 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF/G6PD/FASN/INPP4B/PRDX1
## GO:0016032                                                                                                                                                                                                                                                                                                                                                           HSPA1A/AKT1/EGFR/BCL2/AXL/ITGA2/TFRC
## GO:0022414                                                                                                                                                                                                                                                                   RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/KIT/EGFR/PTGS2/BCL2/AXL/MSH2/CASP3/BCL2L11/CCNE1/MSH6/ITGA2/PIK3CA
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    47     47/68
## GO:0044423 GO:0044423           virion component     0      0/68
## GO:0110165 GO:0110165 cellular anatomical entity    68     68/68
##                                                                                                                                                                                                                                                                                                                                                                                                    geneID
## GO:0032991                                                                                                                  RB1/HSPA1A/AKT1/MTOR/ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/CHEK1/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/TFRC/RAB11A/RICTOR/TP53BP1
## GO:0044423                                                                                                                                                                                                                                                                                                                                                                                               
## GO:0110165 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/PIK3CA/PRKCA/MAPK1/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF/G6PD/FASN/INPP4B/PRDX1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/28
## GO:0003824 GO:0003824           catalytic activity    13     13/28
## GO:0005198 GO:0005198 structural molecule activity     0      0/28
## GO:0005215 GO:0005215         transporter activity     1      1/28
## GO:0005488 GO:0005488                      binding    28     28/28
## GO:0009055 GO:0009055   electron transfer activity     0      0/28
##                                                                                                                                                        geneID
## GO:0003774                                                                                                                                                   
## GO:0003824                                                                                AKT2/AKT1/XIAP/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/CCND1/CDKN1A/NCOA3/VHL
## GO:0005198                                                                                                                                                   
## GO:0005215                                                                                                                                               BCL2
## GO:0005488 AKT2/BCL2/MYC/AKT1/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NF2/NCOA3/ITGA2/GAB2/RBM15/TSC1/TTF1/VHL/PREX1
## GO:0009055                                                                                                                                                   
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     7      7/28
## GO:0002376 GO:0002376 immune system process    18     18/28
## GO:0008152 GO:0008152     metabolic process    25     25/28
## GO:0009987 GO:0009987      cellular process    28     28/28
## GO:0016032 GO:0016032         viral process     3      3/28
## GO:0022414 GO:0022414  reproductive process     7      7/28
##                                                                                                                                                        geneID
## GO:0000003                                                                                                                BCL2/AKT1/BCL2L1/RB1/PTEN/ATM/ITGA2
## GO:0002376                                                     BCL2/MYC/AKT1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/CDKN1A/ITGA2/GAB2/RBM15/TSC1/PREX1
## GO:0008152                  AKT2/BCL2/MYC/AKT1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NF2/NCOA3/ITGA2/RBM15/TSC1/TTF1/VHL/PREX1
## GO:0009987 AKT2/BCL2/MYC/AKT1/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NF2/NCOA3/ITGA2/GAB2/RBM15/TSC1/TTF1/VHL/PREX1
## GO:0016032                                                                                                                                    BCL2/AKT1/ITGA2
## GO:0022414                                                                                                                BCL2/AKT1/BCL2L1/RB1/PTEN/ATM/ITGA2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    14     14/28
## GO:0044423 GO:0044423           virion component     0      0/28
## GO:0110165 GO:0110165 cellular anatomical entity    28     28/28
##                                                                                                                                                        geneID
## GO:0032991                                                                       BCL2/MYC/AKT1/BCL2L1/RB1/ETS1/ARID1A/ATM/CCND1/CDKN1A/NCOA3/ITGA2/RBM15/TSC1
## GO:0044423                                                                                                                                                   
## GO:0110165 AKT2/BCL2/MYC/AKT1/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NF2/NCOA3/ITGA2/GAB2/RBM15/TSC1/TTF1/VHL/PREX1
##                    ID                  Description Count GeneRatio geneID
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/0       
## GO:0003824 GO:0003824           catalytic activity     0       0/0       
## GO:0005198 GO:0005198 structural molecule activity     0       0/0       
## GO:0005215 GO:0005215         transporter activity     0       0/0       
## GO:0005488 GO:0005488                      binding     0       0/0       
## GO:0009055 GO:0009055   electron transfer activity     0       0/0       
##                    ID           Description Count GeneRatio geneID
## GO:0000003 GO:0000003          reproduction     0       0/0       
## GO:0002376 GO:0002376 immune system process     0       0/0       
## GO:0008152 GO:0008152     metabolic process     0       0/0       
## GO:0009987 GO:0009987      cellular process     0       0/0       
## GO:0016032 GO:0016032         viral process     0       0/0       
## GO:0022414 GO:0022414  reproductive process     0       0/0       
##                    ID                Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex     0       0/0       
## GO:0044423 GO:0044423           virion component     0       0/0       
## GO:0110165 GO:0110165 cellular anatomical entity     0       0/0       
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/22
## GO:0003824 GO:0003824           catalytic activity    11     11/22
## GO:0005198 GO:0005198 structural molecule activity     1      1/22
## GO:0005215 GO:0005215         transporter activity     0      0/22
## GO:0005488 GO:0005488                      binding    22     22/22
## GO:0009055 GO:0009055   electron transfer activity     0      0/22
##                                                                                                                              geneID
## GO:0003774                                                                                                                    MYH11
## GO:0003824                                                                CDK1/G6PD/ATM/BRCA2/FASN/INPP4B/VHL/PRDX1/GAPDH/MSH6/MSH2
## GO:0005198                                                                                                                    MYH11
## GO:0005215                                                                                                                         
## GO:0005488 STMN1/CDK1/CCNB1/G6PD/IGFBP2/RBM15/GATA3/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2/PREX1
## GO:0009055                                                                                                                         
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     7      7/22
## GO:0002376 GO:0002376 immune system process    13     13/22
## GO:0008152 GO:0008152     metabolic process    19     19/22
## GO:0009987 GO:0009987      cellular process    22     22/22
## GO:0016032 GO:0016032         viral process     2      2/22
## GO:0022414 GO:0022414  reproductive process     7      7/22
##                                                                                                                              geneID
## GO:0000003                                                                                    CDK1/IGFBP2/GATA3/ATM/BRCA2/MSH6/MSH2
## GO:0002376                                                   G6PD/IGFBP2/RBM15/GATA3/ATM/TSC1/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0008152                    CDK1/CCNB1/G6PD/RBM15/GATA3/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0009987 STMN1/CDK1/CCNB1/G6PD/IGFBP2/RBM15/GATA3/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2/PREX1
## GO:0016032                                                                                                                CDK1/TFRC
## GO:0022414                                                                                    CDK1/IGFBP2/GATA3/ATM/BRCA2/MSH6/MSH2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    13     13/22
## GO:0044423 GO:0044423           virion component     0      0/22
## GO:0110165 GO:0110165 cellular anatomical entity    22     22/22
##                                                                                                                              geneID
## GO:0032991                                                    CDK1/CCNB1/RBM15/GATA3/ATM/BRCA2/TSC1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2
## GO:0044423                                                                                                                         
## GO:0110165 STMN1/CDK1/CCNB1/G6PD/IGFBP2/RBM15/GATA3/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2/PREX1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/73
## GO:0003824 GO:0003824           catalytic activity    43     43/73
## GO:0005198 GO:0005198 structural molecule activity     1      1/73
## GO:0005215 GO:0005215         transporter activity     2      2/73
## GO:0005488 GO:0005488                      binding    73     73/73
## GO:0009055 GO:0009055   electron transfer activity     0      0/73
##                                                                                                                                                                                                                                                                                                                                                                                                                                  geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                                                                                                         MYH9
## GO:0003824                                                                                                                                                                             XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/RAB25/CCND1/PIK3R1/CHEK1/TUBA1B/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/PRKAA1/CASP9/AXL/MSH2/CASP3/CCNE1/MAPK9/RAF1/GAPDH/MSH6/PIK3CA/PRKCA/MAPK1/MAPK3/RAB11A/BRAF
## GO:0005198                                                                                                                                                                                                                                                                                                                                                                                                                       TUBA1B
## GO:0005215                                                                                                                                                                                                                                                                                                                                                                                                                   IGF1R/BCL2
## GO:0005488 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/BCL2L11/CCNE1/MAPK9/RAF1/YAP1/BCL2L1/DVL3/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF
## GO:0009055                                                                                                                                                                                                                                                                                                                                                                                                                             
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    24     24/73
## GO:0002376 GO:0002376 immune system process    41     41/73
## GO:0008152 GO:0008152     metabolic process    64     64/73
## GO:0009987 GO:0009987      cellular process    73     73/73
## GO:0016032 GO:0016032         viral process     7      7/73
## GO:0022414 GO:0022414  reproductive process    24     24/73
##                                                                                                                                                                                                                                                                                                                                                                                                                                  geneID
## GO:0000003                                                                                                                                                                                                                                                                                          RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/KIT/EGFR/PTGS2/BCL2/AXL/MSH2/CASP3/BCL2L11/CCNE1/BCL2L1/MSH6/ITGA2/PIK3CA
## GO:0002376                                                                                                                                                                                         RB1/XIAP/HSPA1A/AKT1/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/PARP1/IGF1R/PIK3R1/KIT/EZH2/BCL2/AXL/MYC/MSH2/CASP3/BCL2L11/MAPK9/RAF1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/GAB2/TP53BP1/BRAF
## GO:0008152                                                       RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/CHEK1/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/BCL2/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/CCNE1/MAPK9/RAF1/YAP1/DVL3/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RICTOR/TP53BP1/BRAF
## GO:0009987 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/BCL2L11/CCNE1/MAPK9/RAF1/YAP1/BCL2L1/DVL3/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF
## GO:0016032                                                                                                                                                                                                                                                                                                                                                                                         HSPA1A/AKT1/EGFR/BCL2/AXL/ITGA2/TFRC
## GO:0022414                                                                                                                                                                                                                                                                                          RB1/AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/IGF1R/CCNE2/KIT/EGFR/PTGS2/BCL2/AXL/MSH2/CASP3/BCL2L11/CCNE1/BCL2L1/MSH6/ITGA2/PIK3CA
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    53     53/73
## GO:0044423 GO:0044423           virion component     0      0/73
## GO:0110165 GO:0110165 cellular anatomical entity    73     73/73
##                                                                                                                                                                                                                                                                                                                                                                                                                                  geneID
## GO:0032991                                                                                                            RB1/HSPA1A/AKT1/MTOR/ETS1/ARID1A/MYH9/CDKN1A/FOXO3/ATM/CASP8/PARP1/IGF1R/CCNE2/CCND1/PIK3R1/CHEK1/SRSF1/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/YBX1/PRKAA1/PXN/BCL2/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/BCL2L11/CCNE1/YAP1/BCL2L1/DVL3/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/TFRC/RAB11A/RICTOR/TP53BP1
## GO:0044423                                                                                                                                                                                                                                                                                                                                                                                                                             
## GO:0110165 RB1/XIAP/HSPA1A/AKT1/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/PARP1/IGF1R/CCNE2/RAB25/CCND1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/KIT/NCOA3/EGFR/EZH2/PTGS2/MET/AKT2/YBX1/PRKAA1/PXN/BCL2/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/BCL2L11/CCNE1/MAPK9/RAF1/YAP1/BCL2L1/DVL3/EIF4E/EIF4G1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/36
## GO:0003824 GO:0003824           catalytic activity    18     18/36
## GO:0005198 GO:0005198 structural molecule activity     1      1/36
## GO:0005215 GO:0005215         transporter activity     2      2/36
## GO:0005488 GO:0005488                      binding    36     36/36
## GO:0009055 GO:0009055   electron transfer activity     0      0/36
##                                                                                                                                                                                                      geneID
## GO:0003774                                                                                                                                                                                                 
## GO:0003824                                                                                                 MET/AKT2/G6PD/KRAS/CCND1/AKT1/IGF1R/XIAP/MAPK8/PTEN/NRAS/PTK2/ATM/MAPK1/CDKN1A/NCOA3/CHEK1/XRCC1
## GO:0005198                                                                                                                                                                                              FN1
## GO:0005215                                                                                                                                                                                       BCL2/IGF1R
## GO:0005488 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/CDKN1A/STAT5A/NF2/NCOA3/FOXO3/CHEK1/FN1/XRCC1/GAB2
## GO:0009055                                                                                                                                                                                                 
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    10     10/36
## GO:0002376 GO:0002376 immune system process    21     21/36
## GO:0008152 GO:0008152     metabolic process    32     32/36
## GO:0009987 GO:0009987      cellular process    36     36/36
## GO:0016032 GO:0016032         viral process     3      3/36
## GO:0022414 GO:0022414  reproductive process    10     10/36
##                                                                                                                                                                                                      geneID
## GO:0000003                                                                                                                                             ESR1/BCL2/AKT1/IGF1R/BCL2L1/RB1/PTEN/ATM/ITGA2/FOXO3
## GO:0002376                                                                                    ESR1/G6PD/BCL2/AKT1/IGF1R/MYC/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/ITGA2/MAPK1/CDKN1A/FOXO3/FN1/GAB2
## GO:0008152                      ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/PTK2/ATM/YWHAZ/ITGA2/MAPK1/YWHAB/CDKN1A/STAT5A/NF2/NCOA3/FOXO3/CHEK1/FN1/XRCC1
## GO:0009987 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/CDKN1A/STAT5A/NF2/NCOA3/FOXO3/CHEK1/FN1/XRCC1/GAB2
## GO:0016032                                                                                                                                                                                  BCL2/AKT1/ITGA2
## GO:0022414                                                                                                                                             ESR1/BCL2/AKT1/IGF1R/BCL2L1/RB1/PTEN/ATM/ITGA2/FOXO3
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    22     22/36
## GO:0044423 GO:0044423           virion component     0      0/36
## GO:0110165 GO:0110165 cellular anatomical entity    36     36/36
##                                                                                                                                                                                                      geneID
## GO:0032991                                                                         ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/ETS1/ARID1A/ATM/ITGA2/PXN/CDKN1A/STAT5A/NCOA3/FOXO3/CHEK1/FN1/XRCC1
## GO:0044423                                                                                                                                                                                                 
## GO:0110165 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/CDKN1A/STAT5A/NF2/NCOA3/FOXO3/CHEK1/FN1/XRCC1/GAB2
##                    ID                  Description Count GeneRatio geneID
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/1       
## GO:0003824 GO:0003824           catalytic activity     0       0/1       
## GO:0005198 GO:0005198 structural molecule activity     0       0/1       
## GO:0005215 GO:0005215         transporter activity     0       0/1       
## GO:0005488 GO:0005488                      binding     1       1/1  PEA15
## GO:0009055 GO:0009055   electron transfer activity     0       0/1       
##                    ID           Description Count GeneRatio geneID
## GO:0000003 GO:0000003          reproduction     0       0/1       
## GO:0002376 GO:0002376 immune system process     0       0/1       
## GO:0008152 GO:0008152     metabolic process     0       0/1       
## GO:0009987 GO:0009987      cellular process     1       1/1  PEA15
## GO:0016032 GO:0016032         viral process     0       0/1       
## GO:0022414 GO:0022414  reproductive process     0       0/1       
##                    ID                Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex     1       1/1  PEA15
## GO:0044423 GO:0044423           virion component     0       0/1       
## GO:0110165 GO:0110165 cellular anatomical entity     1       1/1  PEA15
##                    ID                  Description Count GeneRatio geneID
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/1       
## GO:0003824 GO:0003824           catalytic activity     1       1/1  PARP1
## GO:0005198 GO:0005198 structural molecule activity     0       0/1       
## GO:0005215 GO:0005215         transporter activity     0       0/1       
## GO:0005488 GO:0005488                      binding     1       1/1  PARP1
## GO:0009055 GO:0009055   electron transfer activity     0       0/1       
##                    ID           Description Count GeneRatio geneID
## GO:0000003 GO:0000003          reproduction     1       1/1  PARP1
## GO:0002376 GO:0002376 immune system process     1       1/1  PARP1
## GO:0008152 GO:0008152     metabolic process     1       1/1  PARP1
## GO:0009987 GO:0009987      cellular process     1       1/1  PARP1
## GO:0016032 GO:0016032         viral process     0       0/1       
## GO:0022414 GO:0022414  reproductive process     1       1/1  PARP1
##                    ID                Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex     1       1/1  PARP1
## GO:0044423 GO:0044423           virion component     0       0/1       
## GO:0110165 GO:0110165 cellular anatomical entity     1       1/1  PARP1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/57
## GO:0003824 GO:0003824           catalytic activity    26     26/57
## GO:0005198 GO:0005198 structural molecule activity     3      3/57
## GO:0005215 GO:0005215         transporter activity     2      2/57
## GO:0005488 GO:0005488                      binding    57     57/57
## GO:0009055 GO:0009055   electron transfer activity     0      0/57
##                                                                                                                                                                                                                                                                                                                                           geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                 MYH11
## GO:0003824                                                                                                                                                                                        XIAP/AKT1/ACACA/PTEN/PARP1/EEF2/IGF1R/MAPK1/GSK3A/FASN/PRKCA/RAB11A/CDK1/TYMS/MSH6/PDK1/G6PD/ASNS/ATM/BRCA2/INPP4B/ACVRL1/VHL/PRDX1/GAPDH/MSH2
## GO:0005198                                                                                                                                                                                                                                                                                                                   CTNNA1/COL6A1/MYH11
## GO:0005215                                                                                                                                                                                                                                                                                                                            BCL2/IGF1R
## GO:0005488 RB1/XIAP/AKT1/ACACA/PTEN/BCL2/BCL2L11/PARP1/CTNNA1/EEF2/GATA3/NRG1/IGF1R/MAPK1/TFRC/NDRG1/AKT1S1/RICTOR/TP53BP1/GSK3A/CDH2/FASN/PRKCA/ANLN/STMN1/RAB11A/ETS1/CDK1/TYMS/MSH6/CCNB1/PDK1/FOXM1/COL6A1/STAT5A/YWHAB/ANXA1/PREX1/SQSTM1/G6PD/IGFBP2/ASNS/RBM15/PEA15/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/VHL/AR/PRDX1/XBP1/GAPDH/MYH11/MSH2
## GO:0009055                                                                                                                                                                                                                                                                                                                                      
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    18     18/57
## GO:0002376 GO:0002376 immune system process    27     27/57
## GO:0008152 GO:0008152     metabolic process    47     47/57
## GO:0009987 GO:0009987      cellular process    57     57/57
## GO:0016032 GO:0016032         viral process     5      5/57
## GO:0022414 GO:0022414  reproductive process    18     18/57
##                                                                                                                                                                                                                                                                                                                                           geneID
## GO:0000003                                                                                                                                                                                                                                   RB1/AKT1/PTEN/BCL2/BCL2L11/PARP1/CTNNA1/GATA3/IGF1R/GSK3A/CDK1/MSH6/COL6A1/IGFBP2/ATM/BRCA2/AR/MSH2
## GO:0002376                                                                                                                                                                             RB1/XIAP/AKT1/BCL2/BCL2L11/PARP1/GATA3/IGF1R/MAPK1/TFRC/NDRG1/TP53BP1/PRKCA/ETS1/MSH6/ANXA1/PREX1/SQSTM1/G6PD/IGFBP2/RBM15/ATM/TSC1/PRDX1/XBP1/GAPDH/MSH2
## GO:0008152                                                                RB1/XIAP/AKT1/ACACA/PTEN/BCL2/PARP1/EEF2/GATA3/NRG1/IGF1R/MAPK1/TFRC/AKT1S1/RICTOR/TP53BP1/GSK3A/FASN/PRKCA/ETS1/CDK1/TYMS/MSH6/CCNB1/PDK1/FOXM1/COL6A1/STAT5A/YWHAB/ANXA1/PREX1/SQSTM1/G6PD/ASNS/RBM15/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/VHL/AR/PRDX1/XBP1/GAPDH/MSH2
## GO:0009987 RB1/XIAP/AKT1/ACACA/PTEN/BCL2/BCL2L11/PARP1/CTNNA1/EEF2/GATA3/NRG1/IGF1R/MAPK1/TFRC/NDRG1/AKT1S1/RICTOR/TP53BP1/GSK3A/CDH2/FASN/PRKCA/ANLN/STMN1/RAB11A/ETS1/CDK1/TYMS/MSH6/CCNB1/PDK1/FOXM1/COL6A1/STAT5A/YWHAB/ANXA1/PREX1/SQSTM1/G6PD/IGFBP2/ASNS/RBM15/PEA15/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/VHL/AR/PRDX1/XBP1/GAPDH/MYH11/MSH2
## GO:0016032                                                                                                                                                                                                                                                                                                             AKT1/BCL2/TFRC/GSK3A/CDK1
## GO:0022414                                                                                                                                                                                                                                   RB1/AKT1/PTEN/BCL2/BCL2L11/PARP1/CTNNA1/GATA3/IGF1R/GSK3A/CDK1/MSH6/COL6A1/IGFBP2/ATM/BRCA2/AR/MSH2
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    36     36/57
## GO:0044423 GO:0044423           virion component     0      0/57
## GO:0110165 GO:0110165 cellular anatomical entity    57     57/57
##                                                                                                                                                                                                                                                                                                                                           geneID
## GO:0032991                                                                                                                       RB1/AKT1/BCL2/BCL2L11/PARP1/CTNNA1/EEF2/GATA3/IGF1R/TFRC/AKT1S1/RICTOR/TP53BP1/GSK3A/CDH2/PRKCA/RAB11A/ETS1/CDK1/MSH6/CCNB1/PDK1/FOXM1/COL6A1/STAT5A/RBM15/PEA15/ATM/BRCA2/ACVRL1/TSC1/AR/XBP1/GAPDH/MYH11/MSH2
## GO:0044423                                                                                                                                                                                                                                                                                                                                      
## GO:0110165 RB1/XIAP/AKT1/ACACA/PTEN/BCL2/BCL2L11/PARP1/CTNNA1/EEF2/GATA3/NRG1/IGF1R/MAPK1/TFRC/NDRG1/AKT1S1/RICTOR/TP53BP1/GSK3A/CDH2/FASN/PRKCA/ANLN/STMN1/RAB11A/ETS1/CDK1/TYMS/MSH6/CCNB1/PDK1/FOXM1/COL6A1/STAT5A/YWHAB/ANXA1/PREX1/SQSTM1/G6PD/IGFBP2/ASNS/RBM15/PEA15/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/VHL/AR/PRDX1/XBP1/GAPDH/MYH11/MSH2
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     1      1/83
## GO:0003824 GO:0003824           catalytic activity    46     46/83
## GO:0005198 GO:0005198 structural molecule activity     2      2/83
## GO:0005215 GO:0005215         transporter activity     2      2/83
## GO:0005488 GO:0005488                      binding    83     83/83
## GO:0009055 GO:0009055   electron transfer activity     0      0/83
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                                                                                                                                                                               MYH9
## GO:0003824                                                                                                                                                                                                                  MET/G6PD/KRAS/CCND1/AKT1/IGF1R/XIAP/CDKN1A/HSPA1A/VHL/MTOR/MAPK8/ATM/CASP8/PTEN/NRAS/PTK2/PARP1/RAB25/RAD51/ERCC1/PIK3R1/CHEK1/TUBA1B/KIT/NCOA3/EGFR/EZH2/PTGS2/AKT2/PRKAA1/CASP9/AXL/MSH2/CASP3/CCNE1/MAPK9/RAF1/GAPDH/MSH6/PIK3CA/PRKCA/MAPK1/MAPK3/RAB11A/BRAF
## GO:0005198                                                                                                                                                                                                                                                                                                                                                                                                                                                                         TUBA1B/FN1
## GO:0005215                                                                                                                                                                                                                                                                                                                                                                                                                                                                         BCL2/IGF1R
## GO:0005488 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/RB1/XIAP/CDKN1A/HSPA1A/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/PARP1/CCNE2/RAB25/AR/EIF4E/MAPT/RAD51/ERCC1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/CDKN1B/BCL2L11/KIT/NCOA3/EGFR/EZH2/PTGS2/AKT2/YBX1/PRKAA1/PXN/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/CCNE1/MAPK9/RAF1/YAP1/BCL2L1/DVL3/EIF4G1/FN1/GAPDH/MSH6/ITGA2/SMAD3/SMAD4/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF
## GO:0009055                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    30     30/83
## GO:0002376 GO:0002376 immune system process    46     46/83
## GO:0008152 GO:0008152     metabolic process    74     74/83
## GO:0009987 GO:0009987      cellular process    83     83/83
## GO:0016032 GO:0016032         viral process     7      7/83
## GO:0022414 GO:0022414  reproductive process    30     30/83
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        geneID
## GO:0000003                                                                                                                                                                                                                                                                                                               ESR1/BCL2/AKT1/IGF1R/RB1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/CCNE2/AR/RAD51/ERCC1/CDKN1B/BCL2L11/KIT/EGFR/PTGS2/AXL/MSH2/CASP3/CCNE1/BCL2L1/MSH6/ITGA2/SMAD4/PIK3CA
## GO:0002376                                                                                                                                                                                                                      ESR1/G6PD/BCL2/AKT1/IGF1R/RB1/XIAP/CDKN1A/HSPA1A/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/FOXO3/ATM/CASP8/PTK2/PARP1/MAPT/ERCC1/PIK3R1/BCL2L11/KIT/EZH2/AXL/MYC/MSH2/CASP3/MAPK9/RAF1/FN1/GAPDH/MSH6/ITGA2/SMAD3/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/GAB2/TP53BP1/BRAF
## GO:0008152                                                       ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/RB1/XIAP/CDKN1A/HSPA1A/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/FOXO3/ATM/CASP8/MACC1/PTEN/PTK2/PARP1/CCNE2/AR/EIF4E/MAPT/RAD51/ERCC1/PIK3R1/CHEK1/SRSF1/STAT5A/CDKN1B/KIT/NCOA3/EGFR/EZH2/PTGS2/AKT2/YBX1/PRKAA1/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/CCNE1/MAPK9/RAF1/YAP1/DVL3/EIF4G1/FN1/GAPDH/MSH6/ITGA2/SMAD3/SMAD4/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RICTOR/TP53BP1/BRAF
## GO:0009987 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/RB1/XIAP/CDKN1A/HSPA1A/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/PARP1/CCNE2/RAB25/AR/EIF4E/MAPT/RAD51/ERCC1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/CDKN1B/BCL2L11/KIT/NCOA3/EGFR/EZH2/PTGS2/AKT2/YBX1/PRKAA1/PXN/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/CCNE1/MAPK9/RAF1/YAP1/BCL2L1/DVL3/EIF4G1/FN1/GAPDH/MSH6/ITGA2/SMAD3/SMAD4/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF
## GO:0016032                                                                                                                                                                                                                                                                                                                                                                                                                                               BCL2/AKT1/HSPA1A/EGFR/AXL/ITGA2/TFRC
## GO:0022414                                                                                                                                                                                                                                                                                                               ESR1/BCL2/AKT1/IGF1R/RB1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/PARP1/CCNE2/AR/RAD51/ERCC1/CDKN1B/BCL2L11/KIT/EGFR/PTGS2/AXL/MSH2/CASP3/CCNE1/BCL2L1/MSH6/ITGA2/SMAD4/PIK3CA
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    62     62/83
## GO:0044423 GO:0044423           virion component     0      0/83
## GO:0110165 GO:0110165 cellular anatomical entity    83     83/83
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        geneID
## GO:0032991                                                                                                                 ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/RB1/CDKN1A/HSPA1A/MTOR/ETS1/ARID1A/MYH9/FOXO3/ATM/CASP8/PARP1/CCNE2/AR/EIF4E/MAPT/RAD51/ERCC1/PIK3R1/CHEK1/SRSF1/STAT5A/CDKN1B/BCL2L11/KIT/NCOA3/EGFR/EZH2/PTGS2/YBX1/PRKAA1/PXN/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/CCNE1/YAP1/BCL2L1/DVL3/EIF4G1/FN1/GAPDH/MSH6/ITGA2/SMAD3/SMAD4/PIK3CA/PRKCA/TFRC/RAB11A/RICTOR/TP53BP1
## GO:0044423                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
## GO:0110165 ESR1/MET/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/RB1/XIAP/CDKN1A/HSPA1A/VHL/MTOR/MAPK8/ETS1/ARID1A/BID/MYH9/FOXO3/ATM/CASP8/MACC1/PTEN/NRAS/PTK2/PARP1/CCNE2/RAB25/AR/EIF4E/MAPT/RAD51/ERCC1/PIK3R1/CHEK1/SRSF1/TUBA1B/STAT5A/CDKN1B/BCL2L11/KIT/NCOA3/EGFR/EZH2/PTGS2/AKT2/YBX1/PRKAA1/PXN/E2F1/CASP9/AXL/CDKN2A/MYC/MSH2/CASP3/CCNE1/MAPK9/RAF1/YAP1/BCL2L1/DVL3/EIF4G1/FN1/GAPDH/MSH6/ITGA2/SMAD3/SMAD4/PIK3CA/PRKCA/MAPK1/MAPK3/TFRC/YWHAE/RAB11A/GAB2/ANLN/RICTOR/TP53BP1/BRAF
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/19
## GO:0003824 GO:0003824           catalytic activity    10     10/19
## GO:0005198 GO:0005198 structural molecule activity     0      0/19
## GO:0005215 GO:0005215         transporter activity     0      0/19
## GO:0005488 GO:0005488                      binding    19     19/19
## GO:0009055 GO:0009055   electron transfer activity     0      0/19
##                                                                                                               geneID
## GO:0003774                                                                                                          
## GO:0003824                                                     G6PD/PTEN/ATM/EGFR/INPP4B/ACVRL1/CDK1/VHL/PRDX1/ERCC1
## GO:0005198                                                                                                          
## GO:0005215                                                                                                          
## GO:0005488 G6PD/IGFBP2/RBM15/PTEN/GATA3/PEA15/ATM/EGFR/INPP4B/ACVRL1/TSC1/PDCD4/CDK1/VHL/PRDX1/XBP1/ERCC1/TFRC/PREX1
## GO:0009055                                                                                                          
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     7      7/19
## GO:0002376 GO:0002376 immune system process    11     11/19
## GO:0008152 GO:0008152     metabolic process    17     17/19
## GO:0009987 GO:0009987      cellular process    19     19/19
## GO:0016032 GO:0016032         viral process     3      3/19
## GO:0022414 GO:0022414  reproductive process     7      7/19
##                                                                                                               geneID
## GO:0000003                                                                     IGFBP2/PTEN/GATA3/ATM/EGFR/CDK1/ERCC1
## GO:0002376                                              G6PD/IGFBP2/RBM15/GATA3/ATM/TSC1/PRDX1/XBP1/ERCC1/TFRC/PREX1
## GO:0008152              G6PD/RBM15/PTEN/GATA3/ATM/EGFR/INPP4B/ACVRL1/TSC1/PDCD4/CDK1/VHL/PRDX1/XBP1/ERCC1/TFRC/PREX1
## GO:0009987 G6PD/IGFBP2/RBM15/PTEN/GATA3/PEA15/ATM/EGFR/INPP4B/ACVRL1/TSC1/PDCD4/CDK1/VHL/PRDX1/XBP1/ERCC1/TFRC/PREX1
## GO:0016032                                                                                            EGFR/CDK1/TFRC
## GO:0022414                                                                     IGFBP2/PTEN/GATA3/ATM/EGFR/CDK1/ERCC1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    11     11/19
## GO:0044423 GO:0044423           virion component     0      0/19
## GO:0110165 GO:0110165 cellular anatomical entity    19     19/19
##                                                                                                               geneID
## GO:0032991                                               RBM15/GATA3/PEA15/ATM/EGFR/ACVRL1/TSC1/CDK1/XBP1/ERCC1/TFRC
## GO:0044423                                                                                                          
## GO:0110165 G6PD/IGFBP2/RBM15/PTEN/GATA3/PEA15/ATM/EGFR/INPP4B/ACVRL1/TSC1/PDCD4/CDK1/VHL/PRDX1/XBP1/ERCC1/TFRC/PREX1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0      0/55
## GO:0003824 GO:0003824           catalytic activity    29     29/55
## GO:0005198 GO:0005198 structural molecule activity     2      2/55
## GO:0005215 GO:0005215         transporter activity     2      2/55
## GO:0005488 GO:0005488                      binding    55     55/55
## GO:0009055 GO:0009055   electron transfer activity     0      0/55
##                                                                                                                                                                                                                                                                                                                       geneID
## GO:0003774                                                                                                                                                                                                                                                                                                                  
## GO:0003824                                                                                                                                                MET/AKT2/G6PD/KRAS/CCND1/AKT1/IGF1R/XIAP/TUBA1B/MAPK8/PTEN/NRAS/PTK2/ATM/MAPK1/PIK3R1/CHEK1/CDKN1A/RAF1/PRKAA1/ACACA/NCOA3/CASP9/AXL/CCNE1/MAPK9/PRKCA/MAPK3/XRCC1
## GO:0005198                                                                                                                                                                                                                                                                                                        TUBA1B/FN1
## GO:0005215                                                                                                                                                                                                                                                                                                        BCL2/IGF1R
## GO:0005488 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/XIAP/TUBA1B/ETS1/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/PIK3R1/CHEK1/SRSF1/CDKN1A/STAT5A/RAF1/PRKAA1/ACACA/NF2/NCOA3/E2F1/CASP9/AXL/CDKN2A/CCNE1/MAPK9/FOXO3/CTNNB1/DVL3/FN1/SMAD3/PRKCA/MAPK3/XRCC1/GAB2/WWTR1/TSC2
## GO:0009055                                                                                                                                                                                                                                                                                                                  
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction    13     13/55
## GO:0002376 GO:0002376 immune system process    29     29/55
## GO:0008152 GO:0008152     metabolic process    50     50/55
## GO:0009987 GO:0009987      cellular process    55     55/55
## GO:0016032 GO:0016032         viral process     4      4/55
## GO:0022414 GO:0022414  reproductive process    13     13/55
##                                                                                                                                                                                                                                                                                                                       geneID
## GO:0000003                                                                                                                                                                                                                                             ESR1/BCL2/AKT1/IGF1R/BCL2L1/RB1/PTEN/ATM/ITGA2/AXL/CCNE1/FOXO3/CTNNB1
## GO:0002376                                                                                                                                                      ESR1/G6PD/BCL2/AKT1/IGF1R/MYC/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PIK3R1/CDKN1A/RAF1/AXL/MAPK9/FOXO3/CTNNB1/FN1/SMAD3/PRKCA/MAPK3/GAB2
## GO:0008152                             ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/PTK2/ATM/YWHAZ/ITGA2/MAPK1/YWHAB/PIK3R1/CHEK1/SRSF1/CDKN1A/STAT5A/RAF1/PRKAA1/ACACA/NF2/NCOA3/E2F1/CASP9/AXL/CDKN2A/CCNE1/MAPK9/FOXO3/CTNNB1/DVL3/FN1/SMAD3/PRKCA/MAPK3/XRCC1/WWTR1/TSC2
## GO:0009987 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/XIAP/TUBA1B/ETS1/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/PIK3R1/CHEK1/SRSF1/CDKN1A/STAT5A/RAF1/PRKAA1/ACACA/NF2/NCOA3/E2F1/CASP9/AXL/CDKN2A/CCNE1/MAPK9/FOXO3/CTNNB1/DVL3/FN1/SMAD3/PRKCA/MAPK3/XRCC1/GAB2/WWTR1/TSC2
## GO:0016032                                                                                                                                                                                                                                                                                               BCL2/AKT1/ITGA2/AXL
## GO:0022414                                                                                                                                                                                                                                             ESR1/BCL2/AKT1/IGF1R/BCL2L1/RB1/PTEN/ATM/ITGA2/AXL/CCNE1/FOXO3/CTNNB1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex    36     36/55
## GO:0044423 GO:0044423           virion component     0      0/55
## GO:0110165 GO:0110165 cellular anatomical entity    55     55/55
##                                                                                                                                                                                                                                                                                                                       geneID
## GO:0032991                                                                                                       ESR1/MET/BCL2/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/ETS1/ARID1A/ATM/ITGA2/PXN/PIK3R1/CHEK1/SRSF1/CDKN1A/STAT5A/PRKAA1/NCOA3/E2F1/CASP9/AXL/CDKN2A/CCNE1/FOXO3/CTNNB1/DVL3/FN1/SMAD3/PRKCA/XRCC1/WWTR1/TSC2
## GO:0044423                                                                                                                                                                                                                                                                                                                  
## GO:0110165 ESR1/MET/AKT2/G6PD/BCL2/KRAS/CCND1/NOTCH3/AKT1/IGF1R/MYC/BCL2L1/RB1/XIAP/TUBA1B/ETS1/MAPK8/ARID1A/BID/PTEN/NRAS/PTK2/ATM/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/PIK3R1/CHEK1/SRSF1/CDKN1A/STAT5A/RAF1/PRKAA1/ACACA/NF2/NCOA3/E2F1/CASP9/AXL/CDKN2A/CCNE1/MAPK9/FOXO3/CTNNB1/DVL3/FN1/SMAD3/PRKCA/MAPK3/XRCC1/GAB2/WWTR1/TSC2
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/6
## GO:0003824 GO:0003824           catalytic activity     3       3/6
## GO:0005198 GO:0005198 structural molecule activity     0       0/6
## GO:0005215 GO:0005215         transporter activity     0       0/6
## GO:0005488 GO:0005488                      binding     6       6/6
## GO:0009055 GO:0009055   electron transfer activity     0       0/6
##                                        geneID
## GO:0003774                                   
## GO:0003824                   EGFR/GAPDH/ERCC1
## GO:0005198                                   
## GO:0005215                                   
## GO:0005488 IGFBP2/RBM15/EGFR/TSC1/GAPDH/ERCC1
## GO:0009055                                   
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     3       3/6
## GO:0002376 GO:0002376 immune system process     5       5/6
## GO:0008152 GO:0008152     metabolic process     5       5/6
## GO:0009987 GO:0009987      cellular process     6       6/6
## GO:0016032 GO:0016032         viral process     1       1/6
## GO:0022414 GO:0022414  reproductive process     3       3/6
##                                        geneID
## GO:0000003                  IGFBP2/EGFR/ERCC1
## GO:0002376      IGFBP2/RBM15/TSC1/GAPDH/ERCC1
## GO:0008152        RBM15/EGFR/TSC1/GAPDH/ERCC1
## GO:0009987 IGFBP2/RBM15/EGFR/TSC1/GAPDH/ERCC1
## GO:0016032                               EGFR
## GO:0022414                  IGFBP2/EGFR/ERCC1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     5       5/6
## GO:0044423 GO:0044423           virion component     0       0/6
## GO:0110165 GO:0110165 cellular anatomical entity     6       6/6
##                                        geneID
## GO:0032991        RBM15/EGFR/TSC1/GAPDH/ERCC1
## GO:0044423                                   
## GO:0110165 IGFBP2/RBM15/EGFR/TSC1/GAPDH/ERCC1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/7
## GO:0003824 GO:0003824           catalytic activity     4       4/7
## GO:0005198 GO:0005198 structural molecule activity     0       0/7
## GO:0005215 GO:0005215         transporter activity     0       0/7
## GO:0005488 GO:0005488                      binding     7       7/7
## GO:0009055 GO:0009055   electron transfer activity     0       0/7
##                                            geneID
## GO:0003774                                       
## GO:0003824                   G6PD/ASNS/EGFR/GAPDH
## GO:0005198                                       
## GO:0005215                                       
## GO:0005488 G6PD/ASNS/RBM15/GATA3/EGFR/GAPDH/PREX1
## GO:0009055                                       
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     2       2/7
## GO:0002376 GO:0002376 immune system process     5       5/7
## GO:0008152 GO:0008152     metabolic process     7       7/7
## GO:0009987 GO:0009987      cellular process     7       7/7
## GO:0016032 GO:0016032         viral process     1       1/7
## GO:0022414 GO:0022414  reproductive process     2       2/7
##                                            geneID
## GO:0000003                             GATA3/EGFR
## GO:0002376           G6PD/RBM15/GATA3/GAPDH/PREX1
## GO:0008152 G6PD/ASNS/RBM15/GATA3/EGFR/GAPDH/PREX1
## GO:0009987 G6PD/ASNS/RBM15/GATA3/EGFR/GAPDH/PREX1
## GO:0016032                                   EGFR
## GO:0022414                             GATA3/EGFR
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     4       4/7
## GO:0044423 GO:0044423           virion component     0       0/7
## GO:0110165 GO:0110165 cellular anatomical entity     7       7/7
##                                            geneID
## GO:0032991                 RBM15/GATA3/EGFR/GAPDH
## GO:0044423                                       
## GO:0110165 G6PD/ASNS/RBM15/GATA3/EGFR/GAPDH/PREX1
##                    ID                  Description Count GeneRatio
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/5
## GO:0003824 GO:0003824           catalytic activity     1       1/5
## GO:0005198 GO:0005198 structural molecule activity     0       0/5
## GO:0005215 GO:0005215         transporter activity     0       0/5
## GO:0005488 GO:0005488                      binding     5       5/5
## GO:0009055 GO:0009055   electron transfer activity     0       0/5
##                                 geneID
## GO:0003774                            
## GO:0003824                        CDK1
## GO:0005198                            
## GO:0005215                            
## GO:0005488 ANLN/STMN1/CDK1/CCNB1/FOXM1
## GO:0009055                            
##                    ID           Description Count GeneRatio
## GO:0000003 GO:0000003          reproduction     1       1/5
## GO:0002376 GO:0002376 immune system process     0       0/5
## GO:0008152 GO:0008152     metabolic process     3       3/5
## GO:0009987 GO:0009987      cellular process     5       5/5
## GO:0016032 GO:0016032         viral process     1       1/5
## GO:0022414 GO:0022414  reproductive process     1       1/5
##                                 geneID
## GO:0000003                        CDK1
## GO:0002376                            
## GO:0008152            CDK1/CCNB1/FOXM1
## GO:0009987 ANLN/STMN1/CDK1/CCNB1/FOXM1
## GO:0016032                        CDK1
## GO:0022414                        CDK1
##                    ID                Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex     3       3/5
## GO:0044423 GO:0044423           virion component     0       0/5
## GO:0110165 GO:0110165 cellular anatomical entity     5       5/5
##                                 geneID
## GO:0032991            CDK1/CCNB1/FOXM1
## GO:0044423                            
## GO:0110165 ANLN/STMN1/CDK1/CCNB1/FOXM1
##                    ID                  Description Count GeneRatio geneID
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/0       
## GO:0003824 GO:0003824           catalytic activity     0       0/0       
## GO:0005198 GO:0005198 structural molecule activity     0       0/0       
## GO:0005215 GO:0005215         transporter activity     0       0/0       
## GO:0005488 GO:0005488                      binding     0       0/0       
## GO:0009055 GO:0009055   electron transfer activity     0       0/0       
##                    ID           Description Count GeneRatio geneID
## GO:0000003 GO:0000003          reproduction     0       0/0       
## GO:0002376 GO:0002376 immune system process     0       0/0       
## GO:0008152 GO:0008152     metabolic process     0       0/0       
## GO:0009987 GO:0009987      cellular process     0       0/0       
## GO:0016032 GO:0016032         viral process     0       0/0       
## GO:0022414 GO:0022414  reproductive process     0       0/0       
##                    ID                Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex     0       0/0       
## GO:0044423 GO:0044423           virion component     0       0/0       
## GO:0110165 GO:0110165 cellular anatomical entity     0       0/0       
##                    ID                  Description Count GeneRatio geneID
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/0       
## GO:0003824 GO:0003824           catalytic activity     0       0/0       
## GO:0005198 GO:0005198 structural molecule activity     0       0/0       
## GO:0005215 GO:0005215         transporter activity     0       0/0       
## GO:0005488 GO:0005488                      binding     0       0/0       
## GO:0009055 GO:0009055   electron transfer activity     0       0/0       
##                    ID           Description Count GeneRatio geneID
## GO:0000003 GO:0000003          reproduction     0       0/0       
## GO:0002376 GO:0002376 immune system process     0       0/0       
## GO:0008152 GO:0008152     metabolic process     0       0/0       
## GO:0009987 GO:0009987      cellular process     0       0/0       
## GO:0016032 GO:0016032         viral process     0       0/0       
## GO:0022414 GO:0022414  reproductive process     0       0/0       
##                    ID                Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex     0       0/0       
## GO:0044423 GO:0044423           virion component     0       0/0       
## GO:0110165 GO:0110165 cellular anatomical entity     0       0/0       
##                    ID                  Description Count GeneRatio geneID
## GO:0003774 GO:0003774  cytoskeletal motor activity     0       0/0       
## GO:0003824 GO:0003824           catalytic activity     0       0/0       
## GO:0005198 GO:0005198 structural molecule activity     0       0/0       
## GO:0005215 GO:0005215         transporter activity     0       0/0       
## GO:0005488 GO:0005488                      binding     0       0/0       
## GO:0009055 GO:0009055   electron transfer activity     0       0/0       
##                    ID           Description Count GeneRatio geneID
## GO:0000003 GO:0000003          reproduction     0       0/0       
## GO:0002376 GO:0002376 immune system process     0       0/0       
## GO:0008152 GO:0008152     metabolic process     0       0/0       
## GO:0009987 GO:0009987      cellular process     0       0/0       
## GO:0016032 GO:0016032         viral process     0       0/0       
## GO:0022414 GO:0022414  reproductive process     0       0/0       
##                    ID                Description Count GeneRatio geneID
## GO:0032991 GO:0032991 protein-containing complex     0       0/0       
## GO:0044423 GO:0044423           virion component     0       0/0       
## GO:0110165 GO:0110165 cellular anatomical entity     0       0/0
barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, Factor 1 of 1")

barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, Factor 1 of 2")

barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, Factor 2 of 2")

barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, Factor 1 of 3")

barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, Factor 2 of 3")

barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, Factor 3 of 3")

barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, Factor 1 of 5")

barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, Factor 2 of 5")

barplot(ggo_MF[[9]], title = "groupGO, Molecular Function, Factor 3 of 5")

barplot(ggo_MF[[10]], title = "groupGO, Molecular Function, Factor 4 of 5")

barplot(ggo_MF[[11]], title = "groupGO, Molecular Function, Factor 5 of 5")

barplot(ggo_MF[[12]], title = "groupGO, Molecular Function, Factor 1 of 10")

barplot(ggo_MF[[13]], title = "groupGO, Molecular Function, Factor 2 of 10")

barplot(ggo_MF[[14]], title = "groupGO, Molecular Function, Factor 3 of 10")

barplot(ggo_MF[[15]], title = "groupGO, Molecular Function, Factor 4 of 10")

barplot(ggo_MF[[16]], title = "groupGO, Molecular Function, Factor 5 of 10")

barplot(ggo_MF[[17]], title = "groupGO, Molecular Function, Factor 6 of 10")

barplot(ggo_MF[[18]], title = "groupGO, Molecular Function, Factor 7 of 10")

barplot(ggo_MF[[19]], title = "groupGO, Molecular Function, Factor 8 of 10")

barplot(ggo_MF[[20]], title = "groupGO, Molecular Function, Factor 9 of 10")

barplot(ggo_MF[[21]], title = "groupGO, Molecular Function, Factor 10 of 10")

barplot(ggo_BP[[1]], title = "groupGO, Biological Process, Factor 1 of 1")

barplot(ggo_BP[[2]], title = "groupGO, Biological Process, Factor 1 of 2")

barplot(ggo_BP[[3]], title = "groupGO, Biological Process, Factor 2 of 2")

barplot(ggo_BP[[4]], title = "groupGO, Biological Process, Factor 1 of 3")

barplot(ggo_BP[[5]], title = "groupGO, Biological Process, Factor 2 of 3")

barplot(ggo_BP[[6]], title = "groupGO, Biological Process, Factor 3 of 3")

barplot(ggo_BP[[7]], title = "groupGO, Biological Process, Factor 1 of 5")

barplot(ggo_BP[[8]], title = "groupGO, Biological Process, Factor 2 of 5")

barplot(ggo_BP[[9]], title = "groupGO, Biological Process, Factor 3 of 5")

barplot(ggo_BP[[10]], title = "groupGO, Biological Process, Factor 4 of 5")

barplot(ggo_BP[[11]], title = "groupGO, Biological Process, Factor 5 of 5")

barplot(ggo_BP[[12]], title = "groupGO, Biological Process, Factor 1 of 10")

barplot(ggo_BP[[13]], title = "groupGO, Biological Process, Factor 2 of 10")

barplot(ggo_BP[[14]], title = "groupGO, Biological Process, Factor 3 of 10")

barplot(ggo_BP[[15]], title = "groupGO, Biological Process, Factor 4 of 10")

barplot(ggo_BP[[16]], title = "groupGO, Biological Process, Factor 5 of 10")

barplot(ggo_BP[[17]], title = "groupGO, Biological Process, Factor 6 of 10")

barplot(ggo_BP[[18]], title = "groupGO, Biological Process, Factor 7 of 10")

barplot(ggo_BP[[19]], title = "groupGO, Biological Process, Factor 8 of 10")

barplot(ggo_BP[[20]], title = "groupGO, Biological Process, Factor 9 of 10")

barplot(ggo_BP[[21]], title = "groupGO, Biological Process, Factor 10 of 10")

barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, Factor 1 of 1")

barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, Factor 1 of 2")

barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, Factor 2 of 2")

barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, Factor 1 of 3")

barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, Factor 2 of 3")

barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, Factor 3 of 3")

barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, Factor 1 of 5")

barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, Factor 2 of 5")

barplot(ggo_CC[[9]], title = "groupGO, Cellular Component, Factor 3 of 5")

barplot(ggo_CC[[10]], title = "groupGO, Cellular Component, Factor 4 of 5")

barplot(ggo_CC[[11]], title = "groupGO, Cellular Component, Factor 5 of 5")

barplot(ggo_CC[[12]], title = "groupGO, Cellular Component, Factor 1 of 10")

barplot(ggo_CC[[13]], title = "groupGO, Cellular Component, Factor 2 of 10")

barplot(ggo_CC[[14]], title = "groupGO, Cellular Component, Factor 3 of 10")

barplot(ggo_CC[[15]], title = "groupGO, Cellular Component, Factor 4 of 10")

barplot(ggo_CC[[16]], title = "groupGO, Cellular Component, Factor 5 of 10")

barplot(ggo_CC[[17]], title = "groupGO, Cellular Component, Factor 6 of 10")

barplot(ggo_CC[[18]], title = "groupGO, Cellular Component, Factor 7 of 10")

barplot(ggo_CC[[19]], title = "groupGO, Cellular Component, Factor 8 of 10")

barplot(ggo_CC[[20]], title = "groupGO, Cellular Component, Factor 9 of 10")

barplot(ggo_CC[[21]], title = "groupGO, Cellular Component, Factor 10 of 10")

B. GO Over-Representation

ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component


for(z in 1:length(geneNames)){
  print(z)
  input <- geneNames[[z]]
  ego_MF[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "MF",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_BP[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "BP",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
  
  ego_CC[[z]] <- enrichGO(
    gene          = input,
    OrgDb         = org.Hs.eg.db,
    ont           = "CC",
    pAdjustMethod = "BH",
    keyType="SYMBOL",
    pvalueCutoff  = 0.05,
    qvalueCutoff  = 0.05,
    minGSSize     = 2,
    readable      = TRUE)
}
## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## --> No gene can be mapped....
## --> Expected input gene ID: ALG12,PDSS2,RBBP8,GGT5,PIGM,RAD50
## --> return NULL...
## --> No gene can be mapped....
## --> Expected input gene ID: FASTKD2,FST,SPATA22,ACTL9,SUN2,UBE2B
## --> return NULL...
## --> No gene can be mapped....
## --> Expected input gene ID: KAT2B,MTA3,NRIP1,ZNF541,MECOM,SF3B3
## --> return NULL...
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## No gene sets have size between 2 and 500 ...
## --> return NULL...
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19
## --> No gene can be mapped....
## --> Expected input gene ID: TMTC2,ALG1L2,PIGM,LCT,NDUFAB1,DPY19L4
## --> return NULL...
## --> No gene can be mapped....
## --> Expected input gene ID: BRINP1,MAP10,SPIDR,TBATA,PTGFR,ACTL9
## --> return NULL...
## --> No gene can be mapped....
## --> Expected input gene ID: POTEI,HDAC10,TAF1D,ACTB,ZNHIT1,KAT6A
## --> return NULL...
## [1] 20
## --> No gene can be mapped....
## --> Expected input gene ID: PDSS1,DPY19L2,GGT1,ALG3,NDUFAB1,DPY19L2P2
## --> return NULL...
## --> No gene can be mapped....
## --> Expected input gene ID: RAD51D,DMRT1,ORC4,UBE2Q1,IL12B,BASP1
## --> return NULL...
## --> No gene can be mapped....
## --> Expected input gene ID: HDAC11,ING4,CHD5,BRD8,ERCC1,TAF2
## --> return NULL...
## [1] 21
## --> No gene can be mapped....
## --> Expected input gene ID: ALG9,PDSS2,DPY19L2P2,DCLRE1C,TMEM260,ALG1
## --> return NULL...
## --> No gene can be mapped....
## --> Expected input gene ID: ATP8B3,FANCA,NRIP1,NR3C1,PYGO2,NPY5R
## --> return NULL...
## --> No gene can be mapped....
## --> Expected input gene ID: GATAD2B,BRPF3,HDAC6,TADA3,KAT2A,MBD3
## --> return NULL...
for(z in 1:18){ #19-21 don't work
  #print(z)
  print(head(ego_MF[[z]]))
  print(head(ego_BP[[z]]))
  print(head(ego_CC[[z]]))
}
##                    ID                                             Description
## GO:0004674 GO:0004674                protein serine/threonine kinase activity
## GO:0019902 GO:0019902                                     phosphatase binding
## GO:0106310 GO:0106310                          protein serine kinase activity
## GO:0019903 GO:0019903                             protein phosphatase binding
## GO:0035173 GO:0035173                                 histone kinase activity
## GO:0004714 GO:0004714 transmembrane receptor protein tyrosine kinase activity
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0004674     11/52 427/18522 2.219321e-08 6.801858e-06 3.116409e-06
## GO:0019902      8/52 189/18522 5.195320e-08 6.801858e-06 3.116409e-06
## GO:0106310     10/52 363/18522 5.621370e-08 6.801858e-06 3.116409e-06
## GO:0019903      7/52 142/18522 1.345680e-07 1.221205e-05 5.595196e-06
## GO:0035173      4/52  23/18522 4.701052e-07 3.412964e-05 1.563718e-05
## GO:0004714      5/52  60/18522 6.958767e-07 4.117645e-05 1.886582e-05
##                                                                 geneID Count
## GO:0004674 AKT1/MTOR/MAPK8/ATM/CHEK1/EGFR/AKT2/PRKAA1/PRKCA/MAPK1/BRAF    11
## GO:0019902                  MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/MAPK1/YWHAE     8
## GO:0106310      AKT1/MTOR/MAPK8/ATM/CHEK1/AKT2/PRKAA1/PRKCA/MAPK1/BRAF    10
## GO:0019903                        MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/YWHAE     7
## GO:0035173                                      ATM/CHEK1/PRKAA1/PRKCA     4
## GO:0004714                                      IGF1R/KIT/EGFR/MET/AXL     5
##                    ID                                 Description GeneRatio
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     16/52
## GO:0104004 GO:0104004 cellular response to environmental stimulus     16/52
## GO:0018105 GO:0018105             peptidyl-serine phosphorylation     15/52
## GO:0018209 GO:0018209                peptidyl-serine modification     15/52
## GO:0062197 GO:0062197        cellular response to chemical stress     15/52
## GO:0071496 GO:0071496      cellular response to external stimulus     15/52
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0071214 334/18888 3.722278e-16 5.438247e-13 2.239244e-13
## GO:0104004 334/18888 3.722278e-16 5.438247e-13 2.239244e-13
## GO:0018105 282/18888 7.685832e-16 7.486000e-13 3.082423e-13
## GO:0018209 294/18888 1.426578e-15 1.042115e-12 4.290996e-13
## GO:0062197 311/18888 3.277191e-15 1.915191e-12 7.885957e-13
## GO:0071496 335/18888 9.798753e-15 4.771993e-12 1.964908e-12
##                                                                                                  geneID
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PIK3R1/CHEK1/IGF1R/EGFR/PTGS2/AKT2/CASP3/YAP1/ITGA2/TP53BP1
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PIK3R1/CHEK1/IGF1R/EGFR/PTGS2/AKT2/CASP3/YAP1/ITGA2/TP53BP1
## GO:0018105          AKT1/MTOR/MAPK8/ATM/PTEN/EGFR/PTGS2/AKT2/PRKAA1/EIF4G1/PRKCA/MAPK1/TFRC/RICTOR/BRAF
## GO:0018209          AKT1/MTOR/MAPK8/ATM/PTEN/EGFR/PTGS2/AKT2/PRKAA1/EIF4G1/PRKCA/MAPK1/TFRC/RICTOR/BRAF
## GO:0062197              HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/EGFR/EZH2/PTGS2/MET/PRKAA1/PXN/AXL/CASP3/MAPK1
## GO:0071496    MTOR/MAPK8/CDKN1A/FOXO3/CASP8/CHEK1/IGF1R/EGFR/PTGS2/PRKAA1/AXL/EIF4G1/ITGA2/MAPK1/RICTOR
##            Count
## GO:0071214    16
## GO:0104004    16
## GO:0018105    15
## GO:0018209    15
## GO:0062197    15
## GO:0071496    15
##                    ID
## GO:0005925 GO:0005925
## GO:0030055 GO:0030055
## GO:0005826 GO:0005826
## GO:1902911 GO:1902911
## GO:0000781 GO:0000781
## GO:0061695 GO:0061695
##                                                               Description
## GO:0005925                                                 focal adhesion
## GO:0030055                                        cell-substrate junction
## GO:0005826                                    actomyosin contractile ring
## GO:1902911                                         protein kinase complex
## GO:0000781                                   chromosome, telomeric region
## GO:0061695 transferase complex, transferring phosphorus-containing groups
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0005925      9/52 421/19894 1.284721e-06 0.0001691692 9.026737e-05
## GO:0030055      9/52 431/19894 1.559164e-06 0.0001691692 9.026737e-05
## GO:0005826      2/52   4/19894 4.007244e-05 0.0024155554 1.288921e-03
## GO:1902911      5/52 150/19894 4.452637e-05 0.0024155554 1.288921e-03
## GO:0000781      5/52 173/19894 8.763402e-05 0.0038033166 2.029420e-03
## GO:0061695      6/52 308/19894 1.467139e-04 0.0046290010 2.469998e-03
##                                                      geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/EGFR/PXN/ITGA2/MAPK1/YWHAE     9
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/EGFR/PXN/ITGA2/MAPK1/YWHAE     9
## GO:0005826                                        MYH9/ANLN     2
## GO:1902911                  CDKN1A/CCND1/IGF1R/PRKAA1/CCNE1     5
## GO:0000781                      ATM/CHEK1/EZH2/MSH2/TP53BP1     5
## GO:0061695           CDKN1A/CCND1/PIK3R1/IGF1R/PRKAA1/CCNE1     6
##                    ID                               Description GeneRatio
## GO:0032143 GO:0032143          single thymine insertion binding      2/18
## GO:0032137 GO:0032137           guanine/thymine mispair binding      2/18
## GO:0032142 GO:0032142          single guanine insertion binding      2/18
## GO:0032138 GO:0032138 single base insertion or deletion binding      2/18
## GO:0032135 GO:0032135         DNA insertion or deletion binding      2/18
## GO:0032405 GO:0032405                 MutLalpha complex binding      2/18
##            BgRatio       pvalue     p.adjust       qvalue    geneID Count
## GO:0032143 2/18522 8.920088e-07 0.0001239178 5.442812e-05 MSH6/MSH2     2
## GO:0032137 3/18522 2.674485e-06 0.0001239178 5.442812e-05 MSH6/MSH2     2
## GO:0032142 3/18522 2.674485e-06 0.0001239178 5.442812e-05 MSH6/MSH2     2
## GO:0032138 4/18522 5.345889e-06 0.0001857697 8.159515e-05 MSH6/MSH2     2
## GO:0032135 6/18522 1.334933e-05 0.0003092596 1.358353e-04 MSH6/MSH2     2
## GO:0032405 6/18522 1.334933e-05 0.0003092596 1.358353e-04 MSH6/MSH2     2
##                    ID
## GO:0002562 GO:0002562
## GO:0016444 GO:0016444
## GO:0002200 GO:0002200
## GO:0002520 GO:0002520
## GO:0002312 GO:0002312
## GO:0002285 GO:0002285
##                                                                                             Description
## GO:0002562 somatic diversification of immune receptors via germline recombination within a single locus
## GO:0016444                                                               somatic cell DNA recombination
## GO:0002200                                                  somatic diversification of immune receptors
## GO:0002520                                                                    immune system development
## GO:0002312                                                B cell activation involved in immune response
## GO:0002285                                            lymphocyte activation involved in immune response
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0002562      4/18  70/18888 5.088977e-07 0.0002509906 0.0001319869
## GO:0016444      4/18  70/18888 5.088977e-07 0.0002509906 0.0001319869
## GO:0002200      4/18  76/18888 7.095469e-07 0.0002509906 0.0001319869
## GO:0002520      5/18 197/18888 9.001426e-07 0.0002509906 0.0001319869
## GO:0002312      4/18  87/18888 1.223008e-06 0.0002509906 0.0001319869
## GO:0002285      5/18 212/18888 1.292655e-06 0.0002509906 0.0001319869
##                              geneID Count
## GO:0002562       ATM/MSH6/TFRC/MSH2     4
## GO:0016444       ATM/MSH6/TFRC/MSH2     4
## GO:0002200       ATM/MSH6/TFRC/MSH2     4
## GO:0002520 RBM15/ATM/MSH6/TFRC/MSH2     5
## GO:0002312      XBP1/MSH6/TFRC/MSH2     4
## GO:0002285 TSC1/XBP1/MSH6/TFRC/MSH2     5
##                    ID             Description GeneRatio   BgRatio       pvalue
## GO:0032301 GO:0032301       MutSalpha complex      2/18   2/19894 7.732128e-07
## GO:0032300 GO:0032300 mismatch repair complex      2/18  11/19894 4.232193e-05
## GO:0042470 GO:0042470              melanosome      3/18 112/19894 1.332719e-04
## GO:0048770 GO:0048770         pigment granule      3/18 112/19894 1.332719e-04
## GO:0032302 GO:0032302        MutSbeta complex      1/18   2/19894 1.808818e-03
## GO:0061793 GO:0061793  chromatin lock complex      1/18   3/19894 2.712067e-03
##                p.adjust       qvalue          geneID Count
## GO:0032301 7.345522e-05 5.209012e-05       MSH6/MSH2     2
## GO:0032300 2.010292e-03 1.425581e-03       MSH6/MSH2     2
## GO:0042470 3.165208e-03 2.244580e-03 FASN/PRDX1/TFRC     3
## GO:0048770 3.165208e-03 2.244580e-03 FASN/PRDX1/TFRC     3
## GO:0032302 3.436753e-02 2.437144e-02            MSH2     1
## GO:0061793 4.292272e-02 3.043827e-02             RB1     1
##                    ID                              Description GeneRatio
## GO:0019902 GO:0019902                      phosphatase binding      9/60
## GO:0004674 GO:0004674 protein serine/threonine kinase activity     12/60
## GO:0019207 GO:0019207                kinase regulator activity     10/60
## GO:0019903 GO:0019903              protein phosphatase binding      8/60
## GO:0106310 GO:0106310           protein serine kinase activity     11/60
## GO:0019887 GO:0019887        protein kinase regulator activity      9/60
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0019902 189/18522 9.356678e-09 1.578662e-06 7.619938e-07
## GO:0004674 427/18522 9.942813e-09 1.578662e-06 7.619938e-07
## GO:0019207 270/18522 1.456427e-08 1.578662e-06 7.619938e-07
## GO:0019903 142/18522 1.789157e-08 1.578662e-06 7.619938e-07
## GO:0106310 363/18522 2.044899e-08 1.578662e-06 7.619938e-07
## GO:0019887 232/18522 5.515042e-08 3.548010e-06 1.712566e-06
##                                                                        geneID
## GO:0019902                    MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/BCL2/MAPK1/YWHAE
## GO:0004674 AKT1/MTOR/MAPK8/ATM/CHEK1/EGFR/AKT2/PRKAA1/PIK3CA/PRKCA/MAPK1/BRAF
## GO:0019207      AKT1/CDKN1A/CCNE2/CCND1/PIK3R1/EGFR/CASP3/CCNE1/PIK3CA/RICTOR
## GO:0019903                          MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/BCL2/YWHAE
## GO:0106310      AKT1/MTOR/MAPK8/ATM/CHEK1/AKT2/PRKAA1/PIK3CA/PRKCA/MAPK1/BRAF
## GO:0019887             AKT1/CDKN1A/CCNE2/CCND1/EGFR/CASP3/CCNE1/PIK3CA/RICTOR
##            Count
## GO:0019902     9
## GO:0004674    12
## GO:0019207    10
## GO:0019903     8
## GO:0106310    11
## GO:0019887     9
##                    ID                                 Description GeneRatio
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     19/60
## GO:0104004 GO:0104004 cellular response to environmental stimulus     19/60
## GO:0009314 GO:0009314                       response to radiation     20/60
## GO:0062197 GO:0062197        cellular response to chemical stress     17/60
## GO:0009416 GO:0009416                  response to light stimulus     17/60
## GO:0018105 GO:0018105             peptidyl-serine phosphorylation     16/60
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0071214 334/18888 3.213319e-19 5.107571e-16 2.039612e-16
## GO:0104004 334/18888 3.213319e-19 5.107571e-16 2.039612e-16
## GO:0009314 431/18888 1.713984e-18 1.816252e-15 7.252859e-16
## GO:0062197 311/18888 6.348179e-17 5.045215e-14 2.014712e-14
## GO:0009416 321/18888 1.078848e-16 6.859316e-14 2.739139e-14
## GO:0018105 282/18888 3.305462e-16 1.751344e-13 6.993661e-14
##                                                                                                                   geneID
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/MYC/CASP3/YAP1/ITGA2/PIK3CA/TP53BP1
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/MYC/CASP3/YAP1/ITGA2/PIK3CA/TP53BP1
## GO:0009314 AKT1/MAPK8/CDKN1A/ATM/KRAS/PARP1/CCND1/PIK3R1/KIT/EGFR/AKT2/PRKAA1/BCL2/MYC/MSH2/CASP3/YAP1/MSH6/TP53BP1/BRAF
## GO:0062197                  HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/PARP1/EGFR/EZH2/PTGS2/MET/PRKAA1/PXN/AXL/CASP3/PIK3CA/MAPK1
## GO:0009416                  AKT1/MAPK8/CDKN1A/KRAS/PARP1/CCND1/PIK3R1/KIT/EGFR/AKT2/PRKAA1/BCL2/MYC/MSH2/CASP3/MSH6/BRAF
## GO:0018105                      AKT1/MTOR/MAPK8/ATM/PTEN/EGFR/PTGS2/AKT2/PRKAA1/BCL2/EIF4G1/PRKCA/MAPK1/TFRC/RICTOR/BRAF
##            Count
## GO:0071214    19
## GO:0104004    19
## GO:0009314    20
## GO:0062197    17
## GO:0009416    17
## GO:0018105    16
##                    ID
## GO:0061695 GO:0061695
## GO:0005925 GO:0005925
## GO:0030055 GO:0030055
## GO:1902911 GO:1902911
## GO:0032301 GO:0032301
## GO:0031968 GO:0031968
##                                                               Description
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0005925                                                 focal adhesion
## GO:0030055                                        cell-substrate junction
## GO:1902911                                         protein kinase complex
## GO:0032301                                              MutSalpha complex
## GO:0031968                                       organelle outer membrane
##            GeneRatio   BgRatio       pvalue     p.adjust      qvalue
## GO:0061695      8/60 308/19894 3.833410e-06 0.0003217012 0.000167818
## GO:0005925      9/60 421/19894 4.445599e-06 0.0003217012 0.000167818
## GO:0030055      9/60 431/19894 5.375758e-06 0.0003217012 0.000167818
## GO:1902911      6/60 150/19894 5.948983e-06 0.0003217012 0.000167818
## GO:0032301      2/60   2/19894 8.945011e-06 0.0003217012 0.000167818
## GO:0031968      7/60 248/19894 9.457031e-06 0.0003217012 0.000167818
##                                                         geneID Count
## GO:0061695 CDKN1A/IGF1R/CCNE2/CCND1/PIK3R1/PRKAA1/CCNE1/PIK3CA     8
## GO:0005925    HSPA1A/MYH9/KRAS/PTK2/EGFR/PXN/ITGA2/MAPK1/YWHAE     9
## GO:0030055    HSPA1A/MYH9/KRAS/PTK2/EGFR/PXN/ITGA2/MAPK1/YWHAE     9
## GO:1902911               CDKN1A/IGF1R/CCNE2/CCND1/PRKAA1/CCNE1     6
## GO:0032301                                           MSH2/MSH6     2
## GO:0031968            MTOR/FOXO3/CASP8/KRAS/PTGS2/BCL2/BCL2L11     7
##                    ID                              Description GeneRatio
## GO:0019902 GO:0019902                      phosphatase binding      9/68
## GO:0004674 GO:0004674 protein serine/threonine kinase activity     12/68
## GO:0019903 GO:0019903              protein phosphatase binding      8/68
## GO:0019207 GO:0019207                kinase regulator activity     10/68
## GO:0106310 GO:0106310           protein serine kinase activity     11/68
## GO:0140297 GO:0140297 DNA-binding transcription factor binding     12/68
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0019902 189/18522 2.907790e-08 5.335868e-06 2.348076e-06
## GO:0004674 427/18522 4.380221e-08 5.335868e-06 2.348076e-06
## GO:0019903 142/18522 4.909353e-08 5.335868e-06 2.348076e-06
## GO:0019207 270/18522 5.069709e-08 5.335868e-06 2.348076e-06
## GO:0106310 363/18522 7.952219e-08 6.695769e-06 2.946507e-06
## GO:0140297 478/18522 1.492674e-07 8.869803e-06 3.903201e-06
##                                                                        geneID
## GO:0019902                    MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/BCL2/MAPK1/YWHAE
## GO:0004674 AKT1/MTOR/MAPK8/ATM/CHEK1/EGFR/AKT2/PRKAA1/PIK3CA/PRKCA/MAPK1/BRAF
## GO:0019903                          MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/BCL2/YWHAE
## GO:0019207      AKT1/CDKN1A/CCNE2/CCND1/PIK3R1/EGFR/CASP3/CCNE1/PIK3CA/RICTOR
## GO:0106310      AKT1/MTOR/MAPK8/ATM/CHEK1/AKT2/PRKAA1/PIK3CA/PRKCA/MAPK1/BRAF
## GO:0140297 RB1/VHL/ETS1/ARID1A/PARP1/STAT5A/NCOA3/BCL2/MYC/YAP1/EIF4E/TP53BP1
##            Count
## GO:0019902     9
## GO:0004674    12
## GO:0019903     8
## GO:0019207    10
## GO:0106310    11
## GO:0140297    12
##                    ID                                 Description GeneRatio
## GO:0051402 GO:0051402                    neuron apoptotic process     19/68
## GO:0062197 GO:0062197        cellular response to chemical stress     19/68
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     19/68
## GO:0104004 GO:0104004 cellular response to environmental stimulus     19/68
## GO:0009314 GO:0009314                       response to radiation     20/68
## GO:0000082 GO:0000082       G1/S transition of mitotic cell cycle     16/68
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0051402 292/18888 3.710445e-19 1.225189e-15 5.077451e-16
## GO:0062197 311/18888 1.216651e-18 2.008690e-15 8.324451e-16
## GO:0071214 334/18888 4.634435e-18 3.825726e-15 1.585465e-15
## GO:0104004 334/18888 4.634435e-18 3.825726e-15 1.585465e-15
## GO:0009314 431/18888 2.839156e-17 1.874978e-14 7.770321e-15
## GO:0000082 234/18888 1.526461e-16 8.400623e-14 3.481402e-14
##                                                                                                                   geneID
## GO:0051402         RB1/XIAP/BID/FOXO3/ATM/CASP8/KRAS/PARP1/CCND1/AKT2/BCL2/AXL/MSH2/CASP3/BCL2L11/GAPDH/PIK3CA/BRAF/G6PD
## GO:0062197       HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/PARP1/EGFR/EZH2/PTGS2/MET/PRKAA1/PXN/AXL/CASP3/PIK3CA/MAPK1/G6PD/PRDX1
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/MYC/CASP3/YAP1/ITGA2/PIK3CA/TP53BP1
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/MYC/CASP3/YAP1/ITGA2/PIK3CA/TP53BP1
## GO:0009314 AKT1/MAPK8/CDKN1A/ATM/KRAS/PARP1/CCND1/PIK3R1/KIT/EGFR/AKT2/PRKAA1/BCL2/MYC/MSH2/CASP3/YAP1/MSH6/TP53BP1/BRAF
## GO:0000082                         RB1/AKT1/ARID1A/BID/CDKN1A/ATM/PTEN/CCNE2/CCND1/EGFR/EZH2/BCL2/MYC/CCNE1/EIF4E/EIF4G1
##            Count
## GO:0051402    19
## GO:0062197    19
## GO:0071214    19
## GO:0104004    19
## GO:0009314    20
## GO:0000082    16
##                    ID
## GO:1902911 GO:1902911
## GO:0061695 GO:0061695
## GO:0000307 GO:0000307
## GO:0031968 GO:0031968
## GO:0019867 GO:0019867
## GO:0005741 GO:0005741
##                                                               Description
## GO:1902911                                         protein kinase complex
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:0000307             cyclin-dependent protein kinase holoenzyme complex
## GO:0031968                                       organelle outer membrane
## GO:0019867                                                 outer membrane
## GO:0005741                                   mitochondrial outer membrane
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:1902911      7/68 150/19894 7.942399e-07 0.0001029510 5.644241e-05
## GO:0061695      9/68 308/19894 1.005924e-06 0.0001029510 5.644241e-05
## GO:0000307      5/68  56/19894 1.340841e-06 0.0001029510 5.644241e-05
## GO:0031968      8/68 248/19894 2.020319e-06 0.0001029510 5.644241e-05
## GO:0019867      8/68 250/19894 2.144812e-06 0.0001029510 5.644241e-05
## GO:0005741      7/68 219/19894 9.761782e-06 0.0003829512 2.099513e-04
##                                                             geneID Count
## GO:1902911               RB1/CDKN1A/IGF1R/CCNE2/CCND1/PRKAA1/CCNE1     7
## GO:0061695 RB1/CDKN1A/IGF1R/CCNE2/CCND1/PIK3R1/PRKAA1/CCNE1/PIK3CA     9
## GO:0000307                            RB1/CDKN1A/CCNE2/CCND1/CCNE1     5
## GO:0031968            MTOR/BID/FOXO3/CASP8/KRAS/PTGS2/BCL2/BCL2L11     8
## GO:0019867            MTOR/BID/FOXO3/CASP8/KRAS/PTGS2/BCL2/BCL2L11     8
## GO:0005741                  MTOR/BID/FOXO3/CASP8/KRAS/BCL2/BCL2L11     7
##                    ID                              Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding      8/28
## GO:0051434 GO:0051434                       BH3 domain binding      2/28
## GO:0120283 GO:0120283  protein serine/threonine kinase binding      2/28
## GO:0051400 GO:0051400                        BH domain binding      2/28
## GO:0031625 GO:0031625         ubiquitin protein ligase binding      5/28
## GO:0044389 GO:0044389    ubiquitin-like protein ligase binding      5/28
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0140297 478/18522 3.662033e-07 6.481798e-05 3.315103e-05
## GO:0051434   6/18522 3.293323e-05 2.717739e-03 1.389983e-03
## GO:0120283   7/18522 4.606338e-05 2.717739e-03 1.389983e-03
## GO:0051400   9/18522 7.881811e-05 2.986797e-03 1.527592e-03
## GO:0031625 305/18522 8.437280e-05 2.986797e-03 1.527592e-03
## GO:0044389 324/18522 1.121207e-04 3.039125e-03 1.554355e-03
##                                              geneID Count
## GO:0140297 BCL2/MYC/RB1/ETS1/ARID1A/YWHAZ/NCOA3/VHL     8
## GO:0051434                              BCL2/BCL2L1     2
## GO:0120283                               XIAP/MAPK8     2
## GO:0051400                              BCL2/BCL2L1     2
## GO:0031625                BCL2/RB1/BID/YWHAZ/CDKN1A     5
## GO:0044389                BCL2/RB1/BID/YWHAZ/CDKN1A     5
##                    ID                                         Description
## GO:0000082 GO:0000082               G1/S transition of mitotic cell cycle
## GO:0044843 GO:0044843                    cell cycle G1/S phase transition
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:1902806 GO:1902806      regulation of cell cycle G1/S phase transition
## GO:0051402 GO:0051402                            neuron apoptotic process
## GO:0009314 GO:0009314                               response to radiation
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0000082     10/28 234/18888 7.584848e-13 1.480562e-09 6.187639e-10
## GO:0044843     10/28 262/18888 2.340523e-12 2.284351e-09 9.546871e-10
## GO:2000045      9/28 185/18888 4.014629e-12 2.612185e-09 1.091697e-09
## GO:1902806      9/28 211/18888 1.312373e-11 6.404380e-09 2.676550e-09
## GO:0051402      9/28 292/18888 2.381356e-10 9.296814e-08 3.885370e-08
## GO:0009314     10/28 431/18888 3.135912e-10 1.020217e-07 4.263740e-08
##                                                           geneID Count
## GO:0000082    BCL2/MYC/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A    10
## GO:0044843    BCL2/MYC/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A    10
## GO:2000045        BCL2/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     9
## GO:1902806        BCL2/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A     9
## GO:0051402          AKT2/BCL2/BCL2L1/RB1/XIAP/BID/KRAS/ATM/CCND1     9
## GO:0009314 AKT2/BCL2/MYC/AKT1/BCL2L1/MAPK8/KRAS/ATM/CCND1/CDKN1A    10
##                    ID                                        Description
## GO:0005938 GO:0005938                                        cell cortex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0097136 GO:0097136                       Bcl-2 family protein complex
## GO:0005741 GO:0005741                       mitochondrial outer membrane
## GO:0031968 GO:0031968                           organelle outer membrane
## GO:0019867 GO:0019867                                     outer membrane
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0005938      5/28 309/19894 6.414545e-05 0.003499998 0.001946939
## GO:0000307      3/28  56/19894 6.584049e-05 0.003499998 0.001946939
## GO:0097136      2/28  10/19894 8.536580e-05 0.003499998 0.001946939
## GO:0005741      4/28 219/19894 2.377369e-04 0.007310409 0.004066552
## GO:0031968      4/28 248/19894 3.813894e-04 0.008059755 0.004483389
## GO:0019867      4/28 250/19894 3.931588e-04 0.008059755 0.004483389
##                             geneID Count
## GO:0005938 AKT2/AKT1/PTK2/NF2/TSC1     5
## GO:0000307        RB1/CCND1/CDKN1A     3
## GO:0097136             BCL2/BCL2L1     2
## GO:0005741    BCL2/BCL2L1/BID/KRAS     4
## GO:0031968    BCL2/BCL2L1/BID/KRAS     4
## GO:0019867    BCL2/BCL2L1/BID/KRAS     4
## NULL
## NULL
## NULL
##                    ID                               Description GeneRatio
## GO:0032143 GO:0032143          single thymine insertion binding      2/22
## GO:0032137 GO:0032137           guanine/thymine mispair binding      2/22
## GO:0032142 GO:0032142          single guanine insertion binding      2/22
## GO:0032138 GO:0032138 single base insertion or deletion binding      2/22
## GO:0032135 GO:0032135         DNA insertion or deletion binding      2/22
## GO:0032405 GO:0032405                 MutLalpha complex binding      2/22
##            BgRatio       pvalue     p.adjust       qvalue    geneID Count
## GO:0032143 2/18522 1.346758e-06 0.0002314757 0.0001019966 MSH6/MSH2     2
## GO:0032137 3/18522 4.037366e-06 0.0002314757 0.0001019966 MSH6/MSH2     2
## GO:0032142 3/18522 4.037366e-06 0.0002314757 0.0001019966 MSH6/MSH2     2
## GO:0032138 4/18522 8.068919e-06 0.0003469635 0.0001528848 MSH6/MSH2     2
## GO:0032135 6/18522 2.014327e-05 0.0005774403 0.0002544413 MSH6/MSH2     2
## GO:0032405 6/18522 2.014327e-05 0.0005774403 0.0002544413 MSH6/MSH2     2
##                    ID                                       Description
## GO:0010165 GO:0010165                                 response to X-ray
## GO:0002520 GO:0002520                         immune system development
## GO:0002285 GO:0002285 lymphocyte activation involved in immune response
## GO:0051053 GO:0051053      negative regulation of DNA metabolic process
## GO:1903131 GO:1903131                  mononuclear cell differentiation
## GO:0045785 GO:0045785              positive regulation of cell adhesion
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0010165      4/22  28/18888 2.773903e-08 3.925073e-05 1.997210e-05
## GO:0002520      6/22 197/18888 7.744845e-08 5.479478e-05 2.788144e-05
## GO:0002285      6/22 212/18888 1.196329e-07 5.642687e-05 2.871190e-05
## GO:0051053      5/22 142/18888 5.316425e-07 1.702242e-04 8.661587e-05
## GO:1903131      7/22 484/18888 8.486227e-07 1.702242e-04 8.661587e-05
## GO:0045785      7/22 485/18888 8.604413e-07 1.702242e-04 8.661587e-05
##                                           geneID Count
## GO:0010165                  GATA3/ATM/BRCA2/MSH2     4
## GO:0002520        RBM15/GATA3/ATM/MSH6/TFRC/MSH2     6
## GO:0002285        GATA3/TSC1/XBP1/MSH6/TFRC/MSH2     6
## GO:0051053              GATA3/ATM/TTF1/MSH6/MSH2     5
## GO:1903131   GATA3/ATM/FASN/TSC1/XBP1/MSH2/PREX1     7
## GO:0045785 IGFBP2/GATA3/ATM/TSC1/XBP1/TFRC/PREX1     7
##                    ID                  Description GeneRatio   BgRatio
## GO:0032301 GO:0032301            MutSalpha complex      2/22   2/19894
## GO:0097125 GO:0097125       cyclin B1-CDK1 complex      2/22   2/19894
## GO:0042470 GO:0042470                   melanosome      4/22 112/19894
## GO:0048770 GO:0048770              pigment granule      4/22 112/19894
## GO:0000781 GO:0000781 chromosome, telomeric region      4/22 173/19894
## GO:0032300 GO:0032300      mismatch repair complex      2/22  11/19894
##                  pvalue     p.adjust       qvalue                geneID Count
## GO:0032301 1.167400e-06 5.486779e-05 3.747967e-05             MSH6/MSH2     2
## GO:0097125 1.167400e-06 5.486779e-05 3.747967e-05            CDK1/CCNB1     2
## GO:0042470 6.439119e-06 1.513193e-04 1.033648e-04 FASN/PRDX1/MYH11/TFRC     4
## GO:0048770 6.439119e-06 1.513193e-04 1.033648e-04 FASN/PRDX1/MYH11/TFRC     4
## GO:0000781 3.574947e-05 6.720901e-04 4.590985e-04   CDK1/ATM/BRCA2/MSH2     4
## GO:0032300 6.382076e-05 8.750800e-04 5.977590e-04             MSH6/MSH2     2
##                    ID                              Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding     16/73
## GO:0004674 GO:0004674 protein serine/threonine kinase activity     15/73
## GO:0106310 GO:0106310           protein serine kinase activity     14/73
## GO:0019902 GO:0019902                      phosphatase binding     11/73
## GO:0019207 GO:0019207                kinase regulator activity     11/73
## GO:0019887 GO:0019887        protein kinase regulator activity     10/73
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0140297 478/18522 4.115363e-11 1.650260e-08 7.754210e-09
## GO:0004674 427/18522 9.278499e-11 1.668472e-08 7.839783e-09
## GO:0106310 363/18522 1.248234e-10 1.668472e-08 7.839783e-09
## GO:0019902 189/18522 1.914199e-10 1.918985e-08 9.016887e-09
## GO:0019207 270/18522 8.246097e-09 6.613370e-07 3.107477e-07
## GO:0019887 232/18522 2.440438e-08 1.631026e-06 7.663830e-07
##                                                                                                geneID
## GO:0140297 RB1/VHL/ETS1/ARID1A/PARP1/STAT5A/NCOA3/BCL2/E2F1/CDKN2A/MYC/YAP1/EIF4E/SMAD3/MAPK3/TP53BP1
## GO:0004674        AKT1/MTOR/MAPK8/ATM/CHEK1/EGFR/AKT2/PRKAA1/MAPK9/RAF1/PIK3CA/PRKCA/MAPK1/MAPK3/BRAF
## GO:0106310             AKT1/MTOR/MAPK8/ATM/CHEK1/AKT2/PRKAA1/MAPK9/RAF1/PIK3CA/PRKCA/MAPK1/MAPK3/BRAF
## GO:0019902                                MAPK8/PTK2/PIK3R1/EGFR/MET/PXN/BCL2/SMAD3/MAPK1/MAPK3/YWHAE
## GO:0019207                       AKT1/CDKN1A/CCNE2/CCND1/PIK3R1/EGFR/CDKN2A/CASP3/CCNE1/PIK3CA/RICTOR
## GO:0019887                              AKT1/CDKN1A/CCNE2/CCND1/EGFR/CDKN2A/CASP3/CCNE1/PIK3CA/RICTOR
##            Count
## GO:0140297    16
## GO:0004674    15
## GO:0106310    14
## GO:0019902    11
## GO:0019207    11
## GO:0019887    10
##                    ID                                 Description GeneRatio
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     22/73
## GO:0104004 GO:0104004 cellular response to environmental stimulus     22/73
## GO:0051402 GO:0051402                    neuron apoptotic process     20/73
## GO:0009314 GO:0009314                       response to radiation     22/73
## GO:0000082 GO:0000082       G1/S transition of mitotic cell cycle     18/73
## GO:0062197 GO:0062197        cellular response to chemical stress     19/73
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0071214 334/18888 1.585558e-21 2.679593e-18 1.126581e-18
## GO:0104004 334/18888 1.585558e-21 2.679593e-18 1.126581e-18
## GO:0051402 292/18888 6.518067e-20 7.343689e-17 3.087505e-17
## GO:0009314 431/18888 3.941464e-19 3.330537e-16 1.400257e-16
## GO:0000082 234/18888 7.352870e-19 4.970540e-16 2.089763e-16
## GO:0062197 311/18888 5.365791e-18 2.702208e-15 1.136089e-15
##                                                                                                                                      geneID
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/CASP9/MYC/CASP3/YAP1/BCL2L1/ITGA2/PIK3CA/MAPK3/TP53BP1
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/PARP1/IGF1R/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/CASP9/MYC/CASP3/YAP1/BCL2L1/ITGA2/PIK3CA/MAPK3/TP53BP1
## GO:0051402                    RB1/XIAP/BID/FOXO3/ATM/CASP8/KRAS/PARP1/CCND1/AKT2/BCL2/CASP9/AXL/MSH2/CASP3/BCL2L11/BCL2L1/GAPDH/PIK3CA/BRAF
## GO:0009314       AKT1/MAPK8/CDKN1A/ATM/KRAS/PARP1/CCND1/PIK3R1/KIT/EGFR/AKT2/PRKAA1/BCL2/CASP9/MYC/MSH2/CASP3/YAP1/BCL2L1/MSH6/TP53BP1/BRAF
## GO:0000082                                RB1/AKT1/ARID1A/BID/CDKN1A/ATM/PTEN/CCNE2/CCND1/EGFR/EZH2/BCL2/E2F1/CDKN2A/MYC/CCNE1/EIF4E/EIF4G1
## GO:0062197                         HSPA1A/AKT1/MTOR/MAPK8/FOXO3/ATM/PARP1/EGFR/EZH2/PTGS2/MET/PRKAA1/PXN/AXL/CASP3/MAPK9/PIK3CA/MAPK1/MAPK3
##            Count
## GO:0071214    22
## GO:0104004    22
## GO:0051402    20
## GO:0009314    22
## GO:0000082    18
## GO:0062197    19
##                    ID
## GO:0031968 GO:0031968
## GO:0019867 GO:0019867
## GO:0005741 GO:0005741
## GO:0031143 GO:0031143
## GO:1902911 GO:1902911
## GO:0061695 GO:0061695
##                                                               Description
## GO:0031968                                       organelle outer membrane
## GO:0019867                                                 outer membrane
## GO:0005741                                   mitochondrial outer membrane
## GO:0031143                                                   pseudopodium
## GO:1902911                                         protein kinase complex
## GO:0061695 transferase complex, transferring phosphorus-containing groups
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0031968     10/73 248/19894 2.359797e-08 3.220903e-06 1.876124e-06
## GO:0019867     10/73 250/19894 2.546168e-08 3.220903e-06 1.876124e-06
## GO:0005741      9/73 219/19894 1.061952e-07 8.955799e-06 5.216609e-06
## GO:0031143      4/73  18/19894 4.910057e-07 3.105611e-05 1.808968e-05
## GO:1902911      7/73 150/19894 1.293568e-06 6.545455e-05 3.812622e-05
## GO:0061695      9/73 308/19894 1.851965e-06 6.908763e-05 4.024243e-05
##                                                              geneID Count
## GO:0031968 MTOR/BID/FOXO3/CASP8/KRAS/PTGS2/BCL2/BCL2L11/RAF1/BCL2L1    10
## GO:0019867 MTOR/BID/FOXO3/CASP8/KRAS/PTGS2/BCL2/BCL2L11/RAF1/BCL2L1    10
## GO:0005741       MTOR/BID/FOXO3/CASP8/KRAS/BCL2/BCL2L11/RAF1/BCL2L1     9
## GO:0031143                                   RAB25/RAF1/MAPK1/MAPK3     4
## GO:1902911                RB1/CDKN1A/IGF1R/CCNE2/CCND1/PRKAA1/CCNE1     7
## GO:0061695  RB1/CDKN1A/IGF1R/CCNE2/CCND1/PIK3R1/PRKAA1/CCNE1/PIK3CA     9
##                    ID                              Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding      9/36
## GO:0019902 GO:0019902                      phosphatase binding      6/36
## GO:0019903 GO:0019903              protein phosphatase binding      5/36
## GO:0051219 GO:0051219                   phosphoprotein binding      4/36
## GO:0051434 GO:0051434                       BH3 domain binding      2/36
## GO:0106310 GO:0106310           protein serine kinase activity      6/36
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0140297 478/18522 2.385785e-07 5.415732e-05 2.536466e-05
## GO:0019902 189/18522 1.574359e-06 1.786897e-04 8.368960e-05
## GO:0019903 142/18522 7.683515e-06 5.813860e-04 2.722930e-04
## GO:0051219  93/18522 3.102105e-05 1.760444e-03 8.245067e-04
## GO:0051434   6/18522 5.482548e-05 1.933580e-03 9.055952e-04
## GO:0106310 363/18522 6.442431e-05 1.933580e-03 9.055952e-04
##                                                      geneID Count
## GO:0140297 ESR1/BCL2/MYC/RB1/ETS1/ARID1A/YWHAZ/STAT5A/NCOA3     9
## GO:0019902                    MET/BCL2/MAPK8/PTK2/MAPK1/PXN     6
## GO:0019903                          MET/BCL2/MAPK8/PTK2/PXN     5
## GO:0051219                            RB1/YWHAZ/MAPK1/YWHAB     4
## GO:0051434                                      BCL2/BCL2L1     2
## GO:0106310                  AKT2/AKT1/MAPK8/ATM/MAPK1/CHEK1     6
##                    ID                                         Description
## GO:0051402 GO:0051402                            neuron apoptotic process
## GO:0000082 GO:0000082               G1/S transition of mitotic cell cycle
## GO:0044843 GO:0044843                    cell cycle G1/S phase transition
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:1902806 GO:1902806      regulation of cell cycle G1/S phase transition
## GO:0071214 GO:0071214               cellular response to abiotic stimulus
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0051402     11/36 292/18888 4.258731e-12 9.624732e-09 3.868721e-09
## GO:0000082     10/36 234/18888 1.347155e-11 1.522285e-08 6.118921e-09
## GO:0044843     10/36 262/18888 4.112067e-11 2.890359e-08 1.161798e-08
## GO:2000045      9/36 185/18888 5.115680e-11 2.890359e-08 1.161798e-08
## GO:1902806      9/36 211/18888 1.655707e-10 7.483798e-08 3.008159e-08
## GO:0071214     10/36 334/18888 4.419187e-10 1.262827e-07 5.076011e-08
##                                                             geneID Count
## GO:0051402 AKT2/G6PD/BCL2/KRAS/CCND1/BCL2L1/RB1/XIAP/BID/ATM/FOXO3    11
## GO:0000082      BCL2/CCND1/AKT1/MYC/RB1/ARID1A/BID/PTEN/ATM/CDKN1A    10
## GO:0044843      BCL2/CCND1/AKT1/MYC/RB1/ARID1A/BID/PTEN/ATM/CDKN1A    10
## GO:2000045          BCL2/CCND1/AKT1/RB1/ARID1A/BID/PTEN/ATM/CDKN1A     9
## GO:1902806          BCL2/CCND1/AKT1/RB1/ARID1A/BID/PTEN/ATM/CDKN1A     9
## GO:0071214 AKT2/IGF1R/MYC/BCL2L1/MAPK8/PTEN/ATM/ITGA2/CDKN1A/CHEK1    10
##                    ID                                        Description
## GO:0005925 GO:0005925                                     focal adhesion
## GO:0030055 GO:0030055                            cell-substrate junction
## GO:0005741 GO:0005741                       mitochondrial outer membrane
## GO:0031968 GO:0031968                           organelle outer membrane
## GO:0019867 GO:0019867                                     outer membrane
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0005925      7/36 421/19894 8.881502e-06 0.0007552391 0.0003974943
## GO:0030055      7/36 431/19894 1.034574e-05 0.0007552391 0.0003974943
## GO:0005741      5/36 219/19894 4.408946e-05 0.0021456872 0.0011293090
## GO:0031968      5/36 248/19894 7.949443e-05 0.0024108652 0.0012688764
## GO:0019867      5/36 250/19894 8.256388e-05 0.0024108652 0.0012688764
## GO:0000307      3/36  56/19894 1.412264e-04 0.0027664851 0.0014560448
##                                           geneID Count
## GO:0005925 KRAS/PTK2/YWHAZ/ITGA2/MAPK1/PXN/YWHAB     7
## GO:0030055 KRAS/PTK2/YWHAZ/ITGA2/MAPK1/PXN/YWHAB     7
## GO:0005741            BCL2/KRAS/BCL2L1/BID/FOXO3     5
## GO:0031968            BCL2/KRAS/BCL2L1/BID/FOXO3     5
## GO:0019867            BCL2/KRAS/BCL2L1/BID/FOXO3     5
## GO:0000307                      CCND1/RB1/CDKN1A     3
## NULL
##                    ID
## GO:1902043 GO:1902043
## GO:0046325 GO:0046325
## GO:0010829 GO:0010829
## GO:1902042 GO:1902042
## GO:1902041 GO:1902041
## GO:2001238 GO:2001238
##                                                                                        Description
## GO:1902043 positive regulation of extrinsic apoptotic signaling pathway via death domain receptors
## GO:0046325                                                   negative regulation of glucose import
## GO:0010829                                  negative regulation of glucose transmembrane transport
## GO:1902042 negative regulation of extrinsic apoptotic signaling pathway via death domain receptors
## GO:1902041          regulation of extrinsic apoptotic signaling pathway via death domain receptors
## GO:2001238                            positive regulation of extrinsic apoptotic signaling pathway
##            GeneRatio  BgRatio       pvalue    p.adjust qvalue geneID Count
## GO:1902043       1/1 12/18888 0.0006353240 0.008894536     NA  PEA15     1
## GO:0046325       1/1 16/18888 0.0008470987 0.008894536     NA  PEA15     1
## GO:0010829       1/1 21/18888 0.0011118170 0.008894536     NA  PEA15     1
## GO:1902042       1/1 31/18888 0.0016412537 0.009847522     NA  PEA15     1
## GO:1902041       1/1 48/18888 0.0025412961 0.010633318     NA  PEA15     1
## GO:2001238       1/1 51/18888 0.0027001271 0.010633318     NA  PEA15     1
##                    ID                    Description GeneRatio   BgRatio
## GO:0005875 GO:0005875 microtubule associated complex       1/1 157/19894
##                 pvalue    p.adjust qvalue geneID Count
## GO:0005875 0.007891827 0.007891827     NA  PEA15     1
##                    ID                                             Description
## GO:0140805 GO:0140805     NAD+-protein-serine ADP-ribosyltransferase activity
## GO:0140294 GO:0140294                 NAD DNA ADP-ribosyltransferase activity
## GO:0140807 GO:0140807  NAD+-protein-glutamate ADP-ribosyltransferase activity
## GO:0140806 GO:0140806 NAD+- protein-aspartate ADP-ribosyltransferase activity
## GO:0140537 GO:0140537              transcription regulator activator activity
## GO:0003950 GO:0003950                    NAD+ ADP-ribosyltransferase activity
##            GeneRatio  BgRatio       pvalue    p.adjust qvalue geneID Count
## GO:0140805       1/1  2/18522 0.0001079797 0.001484721     NA  PARP1     1
## GO:0140294       1/1  3/18522 0.0001619695 0.001484721     NA  PARP1     1
## GO:0140807       1/1  4/18522 0.0002159594 0.001484721     NA  PARP1     1
## GO:0140806       1/1  5/18522 0.0002699492 0.001484721     NA  PARP1     1
## GO:0140537       1/1  8/18522 0.0004319188 0.001900443     NA  PARP1     1
## GO:0003950       1/1 23/18522 0.0012417665 0.003711802     NA  PARP1     1
##                    ID                                          Description
## GO:1903518 GO:1903518    positive regulation of single strand break repair
## GO:1904762 GO:1904762 positive regulation of myofibroblast differentiation
## GO:0030592 GO:0030592                                 DNA ADP-ribosylation
## GO:1903516 GO:1903516             regulation of single strand break repair
## GO:1905051 GO:1905051                   regulation of base-excision repair
## GO:0071932 GO:0071932                            replication fork reversal
##            GeneRatio BgRatio       pvalue    p.adjust qvalue geneID Count
## GO:1903518       1/1 2/18888 0.0001058873 0.005272307     NA  PARP1     1
## GO:1904762       1/1 2/18888 0.0001058873 0.005272307     NA  PARP1     1
## GO:0030592       1/1 3/18888 0.0001588310 0.005272307     NA  PARP1     1
## GO:1903516       1/1 3/18888 0.0001588310 0.005272307     NA  PARP1     1
## GO:1905051       1/1 3/18888 0.0001588310 0.005272307     NA  PARP1     1
## GO:0071932       1/1 4/18888 0.0002117747 0.005272307     NA  PARP1     1
##                    ID                  Description GeneRatio   BgRatio
## GO:0043596 GO:0043596     nuclear replication fork       1/1  41/19894
## GO:0005657 GO:0005657             replication fork       1/1  74/19894
## GO:0035861 GO:0035861  site of double-strand break       1/1  91/19894
## GO:0090734 GO:0090734           site of DNA damage       1/1 123/19894
## GO:0000781 GO:0000781 chromosome, telomeric region       1/1 173/19894
## GO:0000228 GO:0000228           nuclear chromosome       1/1 226/19894
##                 pvalue   p.adjust qvalue geneID Count
## GO:0043596 0.002060923 0.01219798     NA  PARP1     1
## GO:0005657 0.003719714 0.01219798     NA  PARP1     1
## GO:0035861 0.004574243 0.01219798     NA  PARP1     1
## GO:0090734 0.006182769 0.01236554     NA  PARP1     1
## GO:0000781 0.008696089 0.01391374     NA  PARP1     1
## GO:0000228 0.011360209 0.01514695     NA  PARP1     1
##                    ID                              Description GeneRatio
## GO:0045296 GO:0045296                         cadherin binding      9/57
## GO:0032143 GO:0032143         single thymine insertion binding      2/57
## GO:0140297 GO:0140297 DNA-binding transcription factor binding      9/57
## GO:0032137 GO:0032137          guanine/thymine mispair binding      2/57
## GO:0032142 GO:0032142         single guanine insertion binding      2/57
## GO:0035173 GO:0035173                  histone kinase activity      3/57
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0045296 333/18522 7.418914e-07 0.0002737579 0.0001475973
## GO:0032143   2/18522 9.304876e-06 0.0017167495 0.0009255903
## GO:0140297 478/18522 1.409834e-05 0.0017340964 0.0009349428
## GO:0032137   3/18522 2.785936e-05 0.0020560208 0.0011085093
## GO:0032142   3/18522 2.785936e-05 0.0020560208 0.0011085093
## GO:0035173  23/18522 4.684392e-05 0.0025649388 0.0013828938
##                                                        geneID Count
## GO:0045296 CTNNA1/EEF2/NDRG1/CDH2/FASN/ANLN/YWHAB/ANXA1/PRDX1     9
## GO:0032143                                          MSH6/MSH2     2
## GO:0140297    RB1/BCL2/PARP1/GATA3/TP53BP1/ETS1/STAT5A/VHL/AR     9
## GO:0032137                                          MSH6/MSH2     2
## GO:0032142                                          MSH6/MSH2     2
## GO:0035173                                     PRKCA/CDK1/ATM     3
##                    ID                          Description GeneRatio   BgRatio
## GO:0051402 GO:0051402             neuron apoptotic process     13/57 292/18888
## GO:0030879 GO:0030879            mammary gland development     10/57 135/18888
## GO:0051146 GO:0051146 striated muscle cell differentiation     12/57 313/18888
## GO:0048872 GO:0048872       homeostasis of number of cells     12/57 322/18888
## GO:0002520 GO:0002520            immune system development     10/57 197/18888
## GO:0048732 GO:0048732                    gland development     13/57 449/18888
##                  pvalue     p.adjust       qvalue
## GO:0051402 2.941388e-12 8.621207e-09 3.966229e-09
## GO:0030879 8.059497e-12 1.181119e-08 5.433798e-09
## GO:0051146 1.262295e-10 1.233262e-07 5.673683e-08
## GO:0048872 1.749112e-10 1.281662e-07 5.896350e-08
## GO:0002520 3.418142e-10 2.003715e-07 9.218189e-08
## GO:0048732 6.159712e-10 3.009019e-07 1.384314e-07
##                                                                               geneID
## GO:0051402 RB1/XIAP/BCL2/BCL2L11/PARP1/GATA3/AKT1S1/GSK3A/COL6A1/G6PD/ATM/GAPDH/MSH2
## GO:0030879                   AKT1/BCL2L11/GATA3/NRG1/MAPK1/FASN/STAT5A/BRCA2/AR/XBP1
## GO:0051146            RB1/AKT1/BCL2/NRG1/GSK3A/CDH2/CDK1/COL6A1/G6PD/TSC1/XBP1/MYH11
## GO:0048872        RB1/XIAP/AKT1/BCL2/BCL2L11/GATA3/CDH2/ETS1/COL6A1/ANXA1/G6PD/PRDX1
## GO:0002520                 BCL2/BCL2L11/GATA3/MAPK1/TFRC/TP53BP1/MSH6/RBM15/ATM/MSH2
## GO:0048732     AKT1/BCL2/BCL2L11/GATA3/NRG1/MAPK1/FASN/TYMS/STAT5A/ATM/BRCA2/AR/XBP1
##            Count
## GO:0051402    13
## GO:0030879    10
## GO:0051146    12
## GO:0048872    12
## GO:0002520    10
## GO:0048732    13
##                    ID                  Description GeneRatio   BgRatio
## GO:0032301 GO:0032301            MutSalpha complex      2/57   2/19894
## GO:0097125 GO:0097125       cyclin B1-CDK1 complex      2/57   2/19894
## GO:0000781 GO:0000781 chromosome, telomeric region      6/57 173/19894
## GO:0042470 GO:0042470                   melanosome      5/57 112/19894
## GO:0048770 GO:0048770              pigment granule      5/57 112/19894
## GO:1990391 GO:1990391           DNA repair complex      3/57  22/19894
##                  pvalue     p.adjust       qvalue
## GO:0032301 8.065671e-06 0.0007273642 0.0004265245
## GO:0097125 8.065671e-06 0.0007273642 0.0004265245
## GO:0000781 9.963893e-06 0.0007273642 0.0004265245
## GO:0042470 1.714196e-05 0.0007508176 0.0004402776
## GO:0048770 1.714196e-05 0.0007508176 0.0004402776
## GO:1990391 3.304014e-05 0.0012059651 0.0007071749
##                                       geneID Count
## GO:0032301                         MSH6/MSH2     2
## GO:0097125                        CDK1/CCNB1     2
## GO:0000781 PARP1/TP53BP1/CDK1/ATM/BRCA2/MSH2     6
## GO:0042470       TFRC/FASN/YWHAB/PRDX1/MYH11     5
## GO:0048770       TFRC/FASN/YWHAB/PRDX1/MYH11     5
## GO:1990391                 TP53BP1/ATM/BRCA2     3
##                    ID
## GO:0140297 GO:0140297
## GO:0019902 GO:0019902
## GO:0004674 GO:0004674
## GO:0106310 GO:0106310
## GO:0019903 GO:0019903
## GO:0016538 GO:0016538
##                                                                    Description
## GO:0140297                            DNA-binding transcription factor binding
## GO:0019902                                                 phosphatase binding
## GO:0004674                            protein serine/threonine kinase activity
## GO:0106310                                      protein serine kinase activity
## GO:0019903                                         protein phosphatase binding
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0140297     19/83 478/18522 2.598024e-13 1.158719e-10 5.360134e-11
## GO:0019902     13/83 189/18522 2.434097e-12 5.428037e-10 2.510964e-10
## GO:0004674     15/83 427/18522 6.289373e-10 6.862943e-08 3.174739e-08
## GO:0106310     14/83 363/18522 7.479241e-10 6.862943e-08 3.174739e-08
## GO:0019903     10/83 142/18522 7.693883e-10 6.862943e-08 3.174739e-08
## GO:0016538      7/83  50/18522 2.397033e-09 1.775943e-07 8.215361e-08
##                                                                                                              geneID
## GO:0140297 ESR1/BCL2/RB1/VHL/ETS1/ARID1A/PARP1/AR/EIF4E/STAT5A/NCOA3/E2F1/CDKN2A/MYC/YAP1/SMAD3/SMAD4/MAPK3/TP53BP1
## GO:0019902                                  MET/BCL2/MAPK8/PTK2/MAPT/PIK3R1/CDKN1B/EGFR/PXN/SMAD3/MAPK1/MAPK3/YWHAE
## GO:0004674                      AKT1/MTOR/MAPK8/ATM/CHEK1/EGFR/AKT2/PRKAA1/MAPK9/RAF1/PIK3CA/PRKCA/MAPK1/MAPK3/BRAF
## GO:0106310                           AKT1/MTOR/MAPK8/ATM/CHEK1/AKT2/PRKAA1/MAPK9/RAF1/PIK3CA/PRKCA/MAPK1/MAPK3/BRAF
## GO:0019903                                                    MET/BCL2/MAPK8/PTK2/MAPT/PIK3R1/CDKN1B/EGFR/PXN/YWHAE
## GO:0016538                                                             CCND1/CDKN1A/CCNE2/CDKN1B/CDKN2A/CASP3/CCNE1
##            Count
## GO:0140297    19
## GO:0019902    13
## GO:0004674    15
## GO:0106310    14
## GO:0019903    10
## GO:0016538     7
##                    ID                                 Description GeneRatio
## GO:0071214 GO:0071214       cellular response to abiotic stimulus     24/83
## GO:0104004 GO:0104004 cellular response to environmental stimulus     24/83
## GO:0009314 GO:0009314                       response to radiation     24/83
## GO:0051402 GO:0051402                    neuron apoptotic process     21/83
## GO:0062197 GO:0062197        cellular response to chemical stress     21/83
## GO:0000082 GO:0000082       G1/S transition of mitotic cell cycle     19/83
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0071214 334/18888 6.820553e-23 1.250207e-19 5.251826e-20
## GO:0104004 334/18888 6.820553e-23 1.250207e-19 5.251826e-20
## GO:0009314 431/18888 2.798088e-20 3.419264e-17 1.436352e-17
## GO:0051402 292/18888 4.741770e-20 4.345832e-17 1.825581e-17
## GO:0062197 311/18888 1.756370e-19 1.287770e-16 5.409619e-17
## GO:0000082 234/18888 3.550507e-19 2.169360e-16 9.112969e-17
##                                                                                                                                                  geneID
## GO:0071214 IGF1R/CDKN1A/MTOR/MAPK8/ATM/CASP8/PTEN/PARP1/RAD51/ERCC1/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/CASP9/MYC/CASP3/YAP1/BCL2L1/ITGA2/PIK3CA/MAPK3/TP53BP1
## GO:0104004 IGF1R/CDKN1A/MTOR/MAPK8/ATM/CASP8/PTEN/PARP1/RAD51/ERCC1/PIK3R1/CHEK1/EGFR/PTGS2/AKT2/CASP9/MYC/CASP3/YAP1/BCL2L1/ITGA2/PIK3CA/MAPK3/TP53BP1
## GO:0009314       BCL2/KRAS/CCND1/AKT1/CDKN1A/MAPK8/ATM/PARP1/RAD51/ERCC1/PIK3R1/KIT/EGFR/AKT2/PRKAA1/CASP9/MYC/MSH2/CASP3/YAP1/BCL2L1/MSH6/TP53BP1/BRAF
## GO:0051402                           G6PD/BCL2/KRAS/CCND1/RB1/XIAP/BID/FOXO3/ATM/CASP8/PARP1/BCL2L11/AKT2/CASP9/AXL/MSH2/CASP3/BCL2L1/GAPDH/PIK3CA/BRAF
## GO:0062197                           MET/G6PD/AKT1/HSPA1A/MTOR/MAPK8/FOXO3/ATM/PARP1/MAPT/EGFR/EZH2/PTGS2/PRKAA1/PXN/AXL/CASP3/MAPK9/PIK3CA/MAPK1/MAPK3
## GO:0000082                                     BCL2/CCND1/AKT1/RB1/CDKN1A/ARID1A/BID/ATM/PTEN/CCNE2/EIF4E/CDKN1B/EGFR/EZH2/E2F1/CDKN2A/MYC/CCNE1/EIF4G1
##            Count
## GO:0071214    24
## GO:0104004    24
## GO:0009314    24
## GO:0051402    21
## GO:0062197    21
## GO:0000082    19
##                    ID                  Description GeneRatio   BgRatio
## GO:0031968 GO:0031968     organelle outer membrane     10/83 248/19894
## GO:0019867 GO:0019867               outer membrane     10/83 250/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane      9/83 219/19894
## GO:0000781 GO:0000781 chromosome, telomeric region      8/83 173/19894
## GO:0031143 GO:0031143                 pseudopodium      4/83  18/19894
## GO:1902911 GO:1902911       protein kinase complex      7/83 150/19894
##                  pvalue     p.adjust       qvalue
## GO:0031968 8.283767e-08 1.285895e-05 7.613853e-06
## GO:0019867 8.929827e-08 1.285895e-05 7.613853e-06
## GO:0005741 3.269219e-07 3.138451e-05 1.858293e-05
## GO:0000781 6.297686e-07 4.534334e-05 2.684803e-05
## GO:0031143 8.243131e-07 4.748044e-05 2.811342e-05
## GO:1902911 3.095495e-06 1.485838e-04 8.797724e-05
##                                                              geneID Count
## GO:0031968 BCL2/KRAS/MTOR/BID/FOXO3/CASP8/BCL2L11/PTGS2/RAF1/BCL2L1    10
## GO:0019867 BCL2/KRAS/MTOR/BID/FOXO3/CASP8/BCL2L11/PTGS2/RAF1/BCL2L1    10
## GO:0005741       BCL2/KRAS/MTOR/BID/FOXO3/CASP8/BCL2L11/RAF1/BCL2L1     9
## GO:0000781            ATM/PARP1/RAD51/ERCC1/CHEK1/EZH2/MSH2/TP53BP1     8
## GO:0031143                                   RAB25/RAF1/MAPK1/MAPK3     4
## GO:1902911                CCND1/IGF1R/RB1/CDKN1A/CCNE2/PRKAA1/CCNE1     7
##                    ID
## GO:0106017 GO:0106017
## GO:0030544 GO:0030544
## GO:0001618 GO:0001618
## GO:0140272 GO:0140272
## GO:0052745 GO:0052745
## GO:0035173 GO:0035173
##                                                           Description GeneRatio
## GO:0106017 phosphatidylinositol-3,4-bisphosphate phosphatase activity      2/19
## GO:0030544                                      Hsp70 protein binding      3/19
## GO:0001618                                    virus receptor activity      3/19
## GO:0140272                                  exogenous protein binding      3/19
## GO:0052745                    inositol phosphate phosphatase activity      2/19
## GO:0035173                                    histone kinase activity      2/19
##             BgRatio       pvalue     p.adjust       qvalue         geneID Count
## GO:0106017  4/18522 5.974387e-06 0.0008722605 0.0004213515    PTEN/INPP4B     2
## GO:0030544 51/18522 1.847373e-05 0.0013485820 0.0006514419 TSC1/CDK1/TFRC     3
## GO:0001618 79/18522 6.888881e-05 0.0026107139 0.0012611235 EGFR/CDK1/TFRC     3
## GO:0140272 80/18522 7.152641e-05 0.0026107139 0.0012611235 EGFR/CDK1/TFRC     3
## GO:0052745 18/18522 1.510472e-04 0.0044105795 0.0021305611    PTEN/INPP4B     2
## GO:0035173 23/18522 2.490081e-04 0.0049183110 0.0023758244       ATM/CDK1     2
##                    ID                                       Description
## GO:0045785 GO:0045785              positive regulation of cell adhesion
## GO:0031667 GO:0031667                       response to nutrient levels
## GO:0007584 GO:0007584                              response to nutrient
## GO:0035051 GO:0035051                        cardiocyte differentiation
## GO:0002520 GO:0002520                         immune system development
## GO:0002285 GO:0002285 lymphocyte activation involved in immune response
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0045785      7/19 485/18888 2.718156e-07 0.0002112691 9.142344e-05
## GO:0031667      7/19 490/18888 2.913520e-07 0.0002112691 9.142344e-05
## GO:0007584      5/19 164/18888 4.892463e-07 0.0002112691 9.142344e-05
## GO:0035051      5/19 165/18888 5.042222e-07 0.0002112691 9.142344e-05
## GO:0002520      5/19 197/18888 1.211298e-06 0.0004060271 1.757020e-04
## GO:0002285      5/19 212/18888 1.738338e-06 0.0004340875 1.878447e-04
##                                           geneID Count
## GO:0045785 IGFBP2/GATA3/ATM/TSC1/XBP1/TFRC/PREX1     7
## GO:0031667 G6PD/IGFBP2/EGFR/TSC1/XBP1/ERCC1/TFRC     7
## GO:0007584           IGFBP2/EGFR/XBP1/ERCC1/TFRC     5
## GO:0035051             G6PD/EGFR/TSC1/PDCD4/CDK1     5
## GO:0002520            RBM15/GATA3/ATM/ERCC1/TFRC     5
## GO:0002285            GATA3/TSC1/XBP1/ERCC1/TFRC     5
##                    ID                                 Description GeneRatio
## GO:0000781 GO:0000781                chromosome, telomeric region      3/19
## GO:0070435 GO:0070435                            Shc-EGFR complex      1/19
## GO:0097122 GO:0097122                      cyclin A2-CDK1 complex      1/19
## GO:0097125 GO:0097125                      cyclin B1-CDK1 complex      1/19
## GO:0030669 GO:0030669  clathrin-coated endocytic vesicle membrane      2/19
## GO:0000110 GO:0000110 nucleotide-excision repair factor 1 complex      1/19
##              BgRatio       pvalue   p.adjust     qvalue         geneID Count
## GO:0000781 173/19894 0.0005652514 0.03700613 0.02048088 ATM/CDK1/ERCC1     3
## GO:0070435   2/19894 0.0019092595 0.03700613 0.02048088           EGFR     1
## GO:0097122   2/19894 0.0019092595 0.03700613 0.02048088           CDK1     1
## GO:0097125   2/19894 0.0019092595 0.03700613 0.02048088           CDK1     1
## GO:0030669  75/19894 0.0023004924 0.03700613 0.02048088      EGFR/TFRC     2
## GO:0000110   3/19894 0.0028625937 0.03700613 0.02048088          ERCC1     1
##                    ID                              Description GeneRatio
## GO:0019902 GO:0019902                      phosphatase binding     11/55
## GO:0140297 GO:0140297 DNA-binding transcription factor binding     14/55
## GO:0106310 GO:0106310           protein serine kinase activity     11/55
## GO:0004674 GO:0004674 protein serine/threonine kinase activity     11/55
## GO:0004707 GO:0004707                      MAP kinase activity      4/55
## GO:0019903 GO:0019903              protein phosphatase binding      7/55
##              BgRatio       pvalue     p.adjust       qvalue
## GO:0019902 189/18522 7.547525e-12 2.211425e-09 1.056653e-09
## GO:0140297 478/18522 7.957760e-11 1.165812e-08 5.570432e-09
## GO:0106310 363/18522 7.793334e-09 7.611489e-07 3.636889e-07
## GO:0004674 427/18522 4.131281e-08 3.026163e-06 1.445948e-06
## GO:0004707  16/18522 1.233117e-07 7.226064e-06 3.452727e-06
## GO:0019903 142/18522 2.002443e-07 9.778597e-06 4.672367e-06
##                                                                                     geneID
## GO:0019902                    MET/BCL2/MAPK8/PTK2/MAPK1/PXN/PIK3R1/CTNNB1/SMAD3/MAPK3/TSC2
## GO:0140297 ESR1/BCL2/MYC/RB1/ETS1/ARID1A/YWHAZ/STAT5A/NCOA3/E2F1/CDKN2A/CTNNB1/SMAD3/MAPK3
## GO:0106310                   AKT2/AKT1/MAPK8/ATM/MAPK1/CHEK1/RAF1/PRKAA1/MAPK9/PRKCA/MAPK3
## GO:0004674                   AKT2/AKT1/MAPK8/ATM/MAPK1/CHEK1/RAF1/PRKAA1/MAPK9/PRKCA/MAPK3
## GO:0004707                                                         MAPK8/MAPK1/MAPK9/MAPK3
## GO:0019903                                           MET/BCL2/MAPK8/PTK2/PXN/PIK3R1/CTNNB1
##            Count
## GO:0019902    11
## GO:0140297    14
## GO:0106310    11
## GO:0004674    11
## GO:0004707     4
## GO:0019903     7
##                    ID                                         Description
## GO:0051402 GO:0051402                            neuron apoptotic process
## GO:0000082 GO:0000082               G1/S transition of mitotic cell cycle
## GO:1901653 GO:1901653                        cellular response to peptide
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:0071375 GO:0071375       cellular response to peptide hormone stimulus
## GO:0044843 GO:0044843                    cell cycle G1/S phase transition
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0051402     14/55 292/18888 8.050039e-14 1.127091e-10 4.913583e-11
## GO:0000082     13/55 234/18888 1.061998e-13 1.127091e-10 4.913583e-11
## GO:1901653     15/55 376/18888 1.336328e-13 1.127091e-10 4.913583e-11
## GO:2000045     12/55 185/18888 1.654398e-13 1.127091e-10 4.913583e-11
## GO:0071375     14/55 311/18888 1.908383e-13 1.127091e-10 4.913583e-11
## GO:0044843     13/55 262/18888 4.517177e-13 1.926300e-10 8.397758e-11
##                                                                                         geneID
## GO:0051402            AKT2/G6PD/BCL2/KRAS/CCND1/BCL2L1/RB1/XIAP/BID/ATM/CASP9/AXL/FOXO3/CTNNB1
## GO:0000082                BCL2/CCND1/AKT1/MYC/RB1/ARID1A/BID/PTEN/ATM/CDKN1A/E2F1/CDKN2A/CCNE1
## GO:1901653 AKT2/AKT1/IGF1R/RB1/PTK2/MAPK1/PXN/PIK3R1/STAT5A/RAF1/PRKAA1/FOXO3/PRKCA/MAPK3/TSC2
## GO:2000045                    BCL2/CCND1/AKT1/RB1/ARID1A/BID/PTEN/ATM/CDKN1A/E2F1/CDKN2A/CCNE1
## GO:0071375       AKT2/AKT1/IGF1R/RB1/PTK2/MAPK1/PXN/PIK3R1/STAT5A/RAF1/PRKAA1/PRKCA/MAPK3/TSC2
## GO:0044843                BCL2/CCND1/AKT1/MYC/RB1/ARID1A/BID/PTEN/ATM/CDKN1A/E2F1/CDKN2A/CCNE1
##            Count
## GO:0051402    14
## GO:0000082    13
## GO:1901653    15
## GO:2000045    12
## GO:0071375    14
## GO:0044843    13
##                    ID                                        Description
## GO:0005925 GO:0005925                                     focal adhesion
## GO:0030055 GO:0030055                            cell-substrate junction
## GO:1902911 GO:1902911                             protein kinase complex
## GO:0090571 GO:0090571  RNA polymerase II transcription repressor complex
## GO:0031143 GO:0031143                                       pseudopodium
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0005925      9/55 421/19894 2.099265e-06 0.0002475384 0.0001446208
## GO:0030055      9/55 431/19894 2.544248e-06 0.0002475384 0.0001446208
## GO:1902911      6/55 150/19894 3.553183e-06 0.0002475384 0.0001446208
## GO:0090571      3/55  15/19894 8.886276e-06 0.0004643079 0.0002712653
## GO:0031143      3/55  18/19894 1.584326e-05 0.0006011223 0.0003511971
## GO:0000307      4/55  56/19894 1.725710e-05 0.0006011223 0.0003511971
##                                                        geneID Count
## GO:0005925 KRAS/PTK2/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/CTNNB1/MAPK3     9
## GO:0030055 KRAS/PTK2/YWHAZ/ITGA2/MAPK1/PXN/YWHAB/CTNNB1/MAPK3     9
## GO:1902911                CCND1/IGF1R/RB1/CDKN1A/PRKAA1/CCNE1     6
## GO:0090571                                   MYC/FOXO3/CTNNB1     3
## GO:0031143                                   MAPK1/RAF1/MAPK3     3
## GO:0000307                             CCND1/RB1/CDKN1A/CCNE1     4
##                    ID
## GO:0004365 GO:0004365
## GO:0043891 GO:0043891
## GO:0019838 GO:0019838
## GO:0005006 GO:0005006
## GO:1990599 GO:1990599
## GO:0048408 GO:0048408
##                                                                              Description
## GO:0004365    glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
## GO:0043891 glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity
## GO:0019838                                                         growth factor binding
## GO:0005006                                     epidermal growth factor receptor activity
## GO:1990599                3' overhang single-stranded DNA endodeoxyribonuclease activity
## GO:0048408                                               epidermal growth factor binding
##            GeneRatio   BgRatio       pvalue   p.adjust      qvalue      geneID
## GO:0004365       1/6   2/18522 0.0006477907 0.01321315 0.003886220       GAPDH
## GO:0043891       1/6   2/18522 0.0006477907 0.01321315 0.003886220       GAPDH
## GO:0019838       2/6 135/18522 0.0007759748 0.01321315 0.003886220 IGFBP2/EGFR
## GO:0005006       1/6   3/18522 0.0009715550 0.01321315 0.003886220        EGFR
## GO:1990599       1/6   3/18522 0.0009715550 0.01321315 0.003886220       ERCC1
## GO:0048408       1/6   4/18522 0.0012952318 0.01467929 0.004317439        EGFR
##            Count
## GO:0004365     1
## GO:0043891     1
## GO:0019838     2
## GO:0005006     1
## GO:1990599     1
## GO:0048408     1
##                    ID                                           Description
## GO:0031667 GO:0031667                           response to nutrient levels
## GO:0007584 GO:0007584                                  response to nutrient
## GO:0048009 GO:0048009 insulin-like growth factor receptor signaling pathway
## GO:0046686 GO:0046686                               response to cadmium ion
## GO:0032355 GO:0032355                                 response to estradiol
## GO:0035606 GO:0035606               peptidyl-cysteine S-trans-nitrosylation
##            GeneRatio   BgRatio       pvalue    p.adjust      qvalue
## GO:0031667       4/6 490/18888 6.439864e-06 0.004274971 0.001719015
## GO:0007584       3/6 164/18888 1.261053e-05 0.004274971 0.001719015
## GO:0048009       2/6  53/18888 1.150515e-04 0.025023966 0.010062424
## GO:0046686       2/6  60/18888 1.476340e-04 0.025023966 0.010062424
## GO:0032355       2/6 115/18888 5.425086e-04 0.034719489 0.013961105
## GO:0035606       1/6   2/18888 6.352399e-04 0.034719489 0.013961105
##                            geneID Count
## GO:0031667 IGFBP2/EGFR/TSC1/ERCC1     4
## GO:0007584      IGFBP2/EGFR/ERCC1     3
## GO:0048009           IGFBP2/ERCC1     2
## GO:0046686             EGFR/ERCC1     2
## GO:0032355            IGFBP2/EGFR     2
## GO:0035606                  GAPDH     1
##                    ID                                 Description GeneRatio
## GO:0031965 GO:0031965                            nuclear membrane       3/6
## GO:0005635 GO:0005635                            nuclear envelope       3/6
## GO:0005811 GO:0005811                               lipid droplet       2/6
## GO:0070435 GO:0070435                            Shc-EGFR complex       1/6
## GO:0000110 GO:0000110 nucleotide-excision repair factor 1 complex       1/6
## GO:0033596 GO:0033596                           TSC1-TSC2 complex       1/6
##              BgRatio       pvalue    p.adjust      qvalue           geneID
## GO:0031965 313/19894 7.448714e-05 0.004022305 0.002430633 RBM15/EGFR/GAPDH
## GO:0005635 498/19894 2.947677e-04 0.007208863 0.004356233 RBM15/EGFR/GAPDH
## GO:0005811 104/19894 4.004924e-04 0.007208863 0.004356233       TSC1/GAPDH
## GO:0070435   2/19894 6.031211e-04 0.008140089 0.004918962             EGFR
## GO:0000110   3/19894 9.045680e-04 0.008140089 0.004918962            ERCC1
## GO:0033596   4/19894 1.205939e-03 0.008140089 0.004918962             TSC1
##            Count
## GO:0031965     3
## GO:0005635     3
## GO:0005811     2
## GO:0070435     1
## GO:0000110     1
## GO:0033596     1
##                    ID
## GO:0050661 GO:0050661
## GO:0004066 GO:0004066
## GO:0004345 GO:0004345
## GO:0004365 GO:0004365
## GO:0043891 GO:0043891
## GO:0005006 GO:0005006
##                                                                              Description
## GO:0050661                                                                  NADP binding
## GO:0004066                          asparagine synthase (glutamine-hydrolyzing) activity
## GO:0004345                                    glucose-6-phosphate dehydrogenase activity
## GO:0004365    glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
## GO:0043891 glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) activity
## GO:0005006                                     epidermal growth factor receptor activity
##            GeneRatio  BgRatio       pvalue   p.adjust      qvalue     geneID
## GO:0050661       2/7 53/18522 0.0001671697 0.01088259 0.005727679 G6PD/GAPDH
## GO:0004066       1/7  2/18522 0.0007557355 0.01088259 0.005727679       ASNS
## GO:0004345       1/7  2/18522 0.0007557355 0.01088259 0.005727679       G6PD
## GO:0004365       1/7  2/18522 0.0007557355 0.01088259 0.005727679      GAPDH
## GO:0043891       1/7  2/18522 0.0007557355 0.01088259 0.005727679      GAPDH
## GO:0005006       1/7  3/18522 0.0011334196 0.01360104 0.007158439       EGFR
##            Count
## GO:0050661     2
## GO:0004066     1
## GO:0004345     1
## GO:0004365     1
## GO:0043891     1
## GO:0005006     1
##                    ID                                    Description GeneRatio
## GO:0072593 GO:0072593      reactive oxygen species metabolic process       3/7
## GO:0051402 GO:0051402                       neuron apoptotic process       3/7
## GO:1902895 GO:1902895     positive regulation of miRNA transcription       2/7
## GO:2000630 GO:2000630 positive regulation of miRNA metabolic process       2/7
## GO:0006801 GO:0006801                   superoxide metabolic process       2/7
## GO:0003281 GO:0003281                 ventricular septum development       2/7
##              BgRatio       pvalue   p.adjust     qvalue           geneID Count
## GO:0072593 238/18888 6.661039e-05 0.02735276 0.01105678  G6PD/EGFR/PREX1     3
## GO:0051402 292/18888 1.222423e-04 0.02735276 0.01105678 G6PD/GATA3/GAPDH     3
## GO:1902895  56/18888 1.795889e-04 0.02735276 0.01105678       GATA3/EGFR     2
## GO:2000630  67/18888 2.573377e-04 0.02735276 0.01105678       GATA3/EGFR     2
## GO:0006801  73/18888 3.055481e-04 0.02735276 0.01105678       EGFR/PREX1     2
## GO:0003281  74/18888 3.139800e-04 0.02735276 0.01105678      RBM15/GATA3     2
##                    ID                                      Description
## GO:0031965 GO:0031965                                 nuclear membrane
## GO:0005635 GO:0005635                                 nuclear envelope
## GO:0070435 GO:0070435                                 Shc-EGFR complex
## GO:0097452 GO:0097452                                     GAIT complex
## GO:0097487 GO:0097487            multivesicular body, internal vesicle
## GO:0036396 GO:0036396 RNA N6-methyladenosine methyltransferase complex
##            GeneRatio   BgRatio       pvalue   p.adjust      qvalue
## GO:0031965       3/7 313/19894 0.0001288323 0.00566862 0.003797162
## GO:0005635       3/7 498/19894 0.0005062513 0.01031981 0.006912794
## GO:0070435       1/7   2/19894 0.0007036236 0.01031981 0.006912794
## GO:0097452       1/7   4/19894 0.0014068229 0.01547505 0.010366063
## GO:0097487       1/7   6/19894 0.0021095979 0.01856446 0.012435525
## GO:0036396       1/7   9/19894 0.0031629656 0.02319508 0.015537375
##                      geneID Count
## GO:0031965 RBM15/EGFR/GAPDH     3
## GO:0005635 RBM15/EGFR/GAPDH     3
## GO:0070435             EGFR     1
## GO:0097452            GAPDH     1
## GO:0097487             EGFR     1
## GO:0036396            RBM15     1
##                    ID
## GO:0005113 GO:0005113
## GO:0008353 GO:0008353
## GO:0061575 GO:0061575
## GO:0035173 GO:0035173
## GO:0140994 GO:0140994
## GO:0004693 GO:0004693
##                                                                    Description
## GO:0005113                                                     patched binding
## GO:0008353           RNA polymerase II CTD heptapeptide repeat kinase activity
## GO:0061575 cyclin-dependent protein serine/threonine kinase activator activity
## GO:0035173                                             histone kinase activity
## GO:0140994        RNA polymerase II CTD heptapeptide repeat modifying activity
## GO:0004693           cyclin-dependent protein serine/threonine kinase activity
##            GeneRatio  BgRatio      pvalue  p.adjust     qvalue geneID Count
## GO:0005113       1/5  8/18522 0.002157962 0.0289896 0.01056301  CCNB1     1
## GO:0008353       1/5 10/18522 0.002696870 0.0289896 0.01056301   CDK1     1
## GO:0061575       1/5 16/18522 0.004312197 0.0289896 0.01056301  CCNB1     1
## GO:0035173       1/5 23/18522 0.006194099 0.0289896 0.01056301   CDK1     1
## GO:0140994       1/5 23/18522 0.006194099 0.0289896 0.01056301   CDK1     1
## GO:0004693       1/5 29/18522 0.007804892 0.0289896 0.01056301   CDK1     1
##                    ID
## GO:1905448 GO:1905448
## GO:1905446 GO:1905446
## GO:0044772 GO:0044772
## GO:0000086 GO:0000086
## GO:0044839 GO:0044839
## GO:1902850 GO:1902850
##                                                                              Description
## GO:1905448 positive regulation of mitochondrial ATP synthesis coupled electron transport
## GO:1905446          regulation of mitochondrial ATP synthesis coupled electron transport
## GO:0044772                                           mitotic cell cycle phase transition
## GO:0000086                                         G2/M transition of mitotic cell cycle
## GO:0044839                                              cell cycle G2/M phase transition
## GO:1902850                     microtubule cytoskeleton organization involved in mitosis
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:1905448       2/5   4/18888 3.363104e-07 0.0001069467 2.584280e-05
## GO:1905446       2/5   7/18888 1.176712e-06 0.0001668324 4.031369e-05
## GO:0044772       4/5 451/18888 1.573891e-06 0.0001668324 4.031369e-05
## GO:0000086       3/5 136/18888 3.613177e-06 0.0002872476 6.941103e-05
## GO:0044839       3/5 152/18888 5.049737e-06 0.0003211632 7.760648e-05
## GO:1902850       3/5 164/18888 6.345810e-06 0.0003363279 8.127090e-05
##                           geneID Count
## GO:1905448            CDK1/CCNB1     2
## GO:1905446            CDK1/CCNB1     2
## GO:0044772 ANLN/CDK1/CCNB1/FOXM1     4
## GO:0000086      CDK1/CCNB1/FOXM1     3
## GO:0044839      CDK1/CCNB1/FOXM1     3
## GO:1902850      STMN1/CDK1/CCNB1     3
##                    ID                                        Description
## GO:0097125 GO:0097125                             cyclin B1-CDK1 complex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:1902554 GO:1902554            serine/threonine protein kinase complex
## GO:0097122 GO:0097122                             cyclin A2-CDK1 complex
## GO:1902911 GO:1902911                             protein kinase complex
## GO:0005826 GO:0005826                        actomyosin contractile ring
##            GeneRatio   BgRatio       pvalue     p.adjust       qvalue
## GO:0097125       2/5   2/19894 5.053678e-08 1.364493e-06 1.595898e-07
## GO:0000307       2/5  56/19894 7.740495e-05 1.044967e-03 1.222183e-04
## GO:1902554       2/5 136/19894 4.577086e-04 3.004513e-03 3.514051e-04
## GO:0097122       1/5   2/19894 5.026136e-04 3.004513e-03 3.514051e-04
## GO:1902911       2/5 150/19894 5.563914e-04 3.004513e-03 3.514051e-04
## GO:0005826       1/5   4/19894 1.005025e-03 3.993377e-03 4.670617e-04
##                geneID Count
## GO:0097125 CDK1/CCNB1     2
## GO:0000307 CDK1/CCNB1     2
## GO:1902554 CDK1/CCNB1     2
## GO:0097122       CDK1     1
## GO:1902911 CDK1/CCNB1     2
## GO:0005826       ANLN     1
barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, Factor 1 of 1")

barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, Factor 1 of 2")

barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, Factor 2 of 2")

barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, Factor 1 of 3")

barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, Factor 2 of 3")

#barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, Factor 3 of 3")
barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, Factor 1 of 5")

barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, Factor 2 of 5")

barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, Factor 3 of 5")

#barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, Factor 4 of 5")
barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, Factor 5 of 5")

barplot(ego_MF[[12]], title = "enrichGO, Molecular Function, Factor 1 of 10")

barplot(ego_MF[[13]], title = "enrichGO, Molecular Function, Factor 2 of 10")

barplot(ego_MF[[14]], title = "enrichGO, Molecular Function, Factor 3 of 10")

barplot(ego_MF[[15]], title = "enrichGO, Molecular Function, Factor 4 of 10")

barplot(ego_MF[[16]], title = "enrichGO, Molecular Function, Factor 5 of 10")

barplot(ego_MF[[17]], title = "enrichGO, Molecular Function, Factor 6 of 10")

barplot(ego_MF[[18]], title = "enrichGO, Molecular Function, Factor 7 of 10")

#barplot(ego_MF[[19]], title = "enrichGO, Molecular Function, Factor 8 of 10")
#barplot(ego_MF[[20]], title = "enrichGO, Molecular Function, Factor 9 of 10")
#barplot(ego_MF[[21]], title = "enrichGO, Molecular Function, Factor 10 of 10")

barplot(ego_BP[[1]], title = "enrichGO, Biological Process, Factor 1 of 1")

barplot(ego_BP[[2]], title = "enrichGO, Biological Process, Factor 1 of 2")

barplot(ego_BP[[3]], title = "enrichGO, Biological Process, Factor 2 of 2")

barplot(ego_BP[[4]], title = "enrichGO, Biological Process, Factor 1 of 3")

barplot(ego_BP[[5]], title = "enrichGO, Biological Process, Factor 2 of 3")

#barplot(ego_BP[[6]], title = "enrichGO, Biological Process, Factor 3 of 3")
barplot(ego_BP[[7]], title = "enrichGO, Biological Process, Factor 1 of 5")

barplot(ego_BP[[8]], title = "enrichGO, Biological Process, Factor 2 of 5")

barplot(ego_BP[[9]], title = "enrichGO, Biological Process, Factor 3 of 5")

barplot(ego_BP[[10]], title = "enrichGO, Biological Process, Factor 4 of 5")

barplot(ego_BP[[11]], title = "enrichGO, Biological Process, Factor 5 of 5")

barplot(ego_BP[[12]], title = "enrichGO, Biological Process, Factor 1 of 10")

barplot(ego_BP[[13]], title = "enrichGO, Biological Process, Factor 2 of 10")

barplot(ego_BP[[14]], title = "enrichGO, Biological Process, Factor 3 of 10")

barplot(ego_BP[[15]], title = "enrichGO, Biological Process, Factor 4 of 10")

barplot(ego_BP[[16]], title = "enrichGO, Biological Process, Factor 5 of 10")

barplot(ego_BP[[17]], title = "enrichGO, Biological Process, Factor 6 of 10")

barplot(ego_BP[[18]], title = "enrichGO, Biological Process, Factor 7 of 10")

#barplot(ego_BP[[19]], title = "enrichGO, Biological Process, Factor 8 of 10")
#barplot(ego_BP[[20]], title = "enrichGO, Biological Process, Factor 9 of 10")
#barplot(ego_BP[[21]], title = "enrichGO, Biological Process, Factor 10 of 10")

barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, Factor 1 of 1")

barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, Factor 1 of 2")

barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, Factor 2 of 2")

barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, Factor 1 of 3")

barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, Factor 2 of 3")

#barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, Factor 3 of 3")
barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, Factor 1 of 5")

barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, Factor 2 of 5")

barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, Factor 3 of 5")

barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, Factor 4 of 5")

barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, Factor 5 of 5")

barplot(ego_CC[[12]], title = "enrichGO, Cellular Component, Factor 1 of 10")

barplot(ego_CC[[13]], title = "enrichGO, Cellular Component, Factor 2 of 10")

barplot(ego_CC[[14]], title = "enrichGO, Cellular Component, Factor 3 of 10")

barplot(ego_CC[[15]], title = "enrichGO, Cellular Component, Factor 4 of 10")

barplot(ego_CC[[16]], title = "enrichGO, Cellular Component, Factor 5 of 10")

barplot(ego_CC[[17]], title = "enrichGO, Cellular Component, Factor 6 of 10")

barplot(ego_CC[[18]], title = "enrichGO, Cellular Component, Factor 7 of 10")

#barplot(ego_CC[[19]], title = "enrichGO, Cellular Component, Factor 8 of 10")
#barplot(ego_CC[[20]], title = "enrichGO, Cellular Component, Factor 9 of 10")
#barplot(ego_CC[[21]], title = "enrichGO, Cellular Component, Factor 10 of 10")

DAG plots for ego

goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 1")

goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 2")

goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 2")

goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 3")

goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 3")

#goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, Factor 3 of 3")
goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 5")

goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 5")

goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, Factor 3 of 5")

#goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, Factor 4 of 5")
goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, Factor 5 of 5")

goplot(ego_MF[[12]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 10")

goplot(ego_MF[[13]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 10")

goplot(ego_MF[[14]]) + labs(title = "enrichGO, Molecular Function, Factor 3 of 10")

goplot(ego_MF[[15]]) + labs(title = "enrichGO, Molecular Function, Factor 4 of 10")

goplot(ego_MF[[16]]) + labs(title = "enrichGO, Molecular Function, Factor 5 of 10")

goplot(ego_MF[[17]]) + labs(title = "enrichGO, Molecular Function, Factor 6 of 10")

goplot(ego_MF[[18]]) + labs(title = "enrichGO, Molecular Function, Factor 7 of 10")

#goplot(ego_MF[[19]]) + labs(title = "enrichGO, Molecular Function, Factor 8 of 10")
#goplot(ego_MF[[20]]) + labs(title = "enrichGO, Molecular Function, Factor 9 of 10")
#goplot(ego_MF[[21]]) + labs(title = "enrichGO, Molecular Function, Factor 10 of 10")

goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 1")

goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 2")

goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 2")

goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 3")

goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 3")

#goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, Factor 3 of 3")
goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 5")
## Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 5")

goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, Factor 3 of 5")

goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, Factor 4 of 5")

goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, Factor 5 of 5")
## Warning: ggrepel: 78 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[12]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 10")

goplot(ego_BP[[13]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 10")

goplot(ego_BP[[14]]) + labs(title = "enrichGO, Biological Process, Factor 3 of 10")

goplot(ego_BP[[15]]) + labs(title = "enrichGO, Biological Process, Factor 4 of 10")

goplot(ego_BP[[16]]) + labs(title = "enrichGO, Biological Process, Factor 5 of 10")
## Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[17]]) + labs(title = "enrichGO, Biological Process, Factor 6 of 10")
## Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps

goplot(ego_BP[[18]]) + labs(title = "enrichGO, Biological Process, Factor 7 of 10")

#goplot(ego_BP[[19]]) + labs(title = "enrichGO, Biological Process, Factor 8 of 10")
#goplot(ego_BP[[20]]) + labs(title = "enrichGO, Biological Process, Factor 9 of 10")
#goplot(ego_BP[[21]]) + labs(title = "enrichGO, Biological Process, Factor 10 of 10")

goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 1")

goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 2")

goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 2")

goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 3")

goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 3")

#goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, Factor 3 of 3")
goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 5")

goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 5")

goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, Factor 3 of 5")

#goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, Factor 4 of 5")
goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, Factor 5 of 5")

goplot(ego_CC[[12]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 10")

goplot(ego_CC[[13]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 10")

goplot(ego_CC[[14]]) + labs(title = "enrichGO, Cellular Component, Factor 3 of 10")

goplot(ego_CC[[15]]) + labs(title = "enrichGO, Cellular Component, Factor 4 of 10")

goplot(ego_CC[[16]]) + labs(title = "enrichGO, Cellular Component, Factor 5 of 10")

goplot(ego_CC[[17]]) + labs(title = "enrichGO, Cellular Component, Factor 6 of 10")

goplot(ego_CC[[18]]) + labs(title = "enrichGO, Cellular Component, Factor 7 of 10")

#goplot(ego_CC[[19]]) + labs(title = "enrichGO, Cellular Component, Factor 8 of 10")
#goplot(ego_CC[[20]]) + labs(title = "enrichGO, Cellular Component, Factor 9 of 10")
#goplot(ego_CC[[21]]) + labs(title = "enrichGO, Cellular Component, Factor 10 of 10")

3. Export Pathway Analysis result to data

pathway = list("ggo_MF" = ggo_MF,
               "ggo_BP" = ggo_BP,
               "ggo_CC" = ggo_CC,
               "ego_MF" = ego_MF,
               "ego_BP" = ego_BP,
               "ego_CC" = ego_CC)

saveRDS(pathway, file = "data/out_pathway/pathways_mofa_extracted_by_bic.rds")